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Chen C, Yang H, Dong S, You C, Moraïs S, Bayer EA, Liu Y, Xuan J, Cui Q, Mizrahi I, Feng Y. A cellulosomal double-dockerin module from Clostridium thermocellum shows distinct structural and cohesin-binding features. Protein Sci 2024; 33:e4937. [PMID: 38501488 PMCID: PMC10949318 DOI: 10.1002/pro.4937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 03/20/2024]
Abstract
Cellulosomes are intricate cellulose-degrading multi-enzymatic complexes produced by anaerobic bacteria, which are valuable for bioenergy development and biotechnology. Cellulosome assembly relies on the selective interaction between cohesin modules in structural scaffolding proteins (scaffoldins) and dockerin modules in enzymes. Although the number of tandem cohesins in the scaffoldins is believed to determine the complexity of the cellulosomes, tandem dockerins also exist, albeit very rare, in some cellulosomal components whose assembly and functional roles are currently unclear. In this study, we characterized the structure and mode of assembly of a tandem bimodular double-dockerin, which is connected to a putative S8 protease in the cellulosome-producing bacterium, Clostridium thermocellum. Crystal and NMR structures of the double-dockerin revealed two typical type I dockerin folds with significant interactions between them. Interaction analysis by isothermal titration calorimetry and NMR titration experiments revealed that the double-dockerin displays a preference for binding to the cell-wall anchoring scaffoldin ScaD through the first dockerin with a canonical dual-binding mode, while the second dockerin module was unable to bind to any of the tested cohesins. Surprisingly, the double-dockerin showed a much higher affinity to a cohesin from the CipC scaffoldin of Clostridium cellulolyticum than to the resident cohesins from C. thermocellum. These results contribute valuable insights into the structure and assembly of the double-dockerin module, and provide the basis for further functional studies on multiple-dockerin modules and cellulosomal proteases, thus highlighting the complexity and diversity of cellulosomal components.
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Affiliation(s)
- Chao Chen
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hongwu Yang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Present address:
College of PharmacyNankai University, Tongyan Road 38, Haihe Education Park, Jinnan DistrictTianjin 300350China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Cai You
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Sarah Moraïs
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐ShevaIsrael
| | - Edward A. Bayer
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐ShevaIsrael
- Department of Biomolecular SciencesThe Weizmann Institute of ScienceRehovotIsrael
| | - Ya‐Jun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jinsong Xuan
- Department of Biological Science and Engineering, School of Chemical and Biological EngineeringUniversity of Science and Technology BeijingBeijingChina
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
- State Key Laboratory of Microbial TechnologyShandong UniversityQingdaoChina
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the NegevBen‐Gurion University of the NegevBeer‐ShevaIsrael
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic BiologyQingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
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Zhang H, Wang Y, Zhu Y, Huang P, Gao Q, Li X, Chen Z, Liu Y, Jiang J, Gao Y, Huang J, Qin Z. Machine learning and genetic algorithm-guided directed evolution for the development of antimicrobial peptides. J Adv Res 2024:S2090-1232(24)00078-X. [PMID: 38431124 DOI: 10.1016/j.jare.2024.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024] Open
Abstract
INTRODUCTION Antimicrobial peptides (AMPs) are valuable alternatives to traditional antibiotics, possess a variety of potent biological activities and exhibit immunomodulatory effects that alleviate difficult-to-treat infections. Clarifying the structure-activity relationships of AMPs can direct the synthesis of desirable peptide therapeutics. OBJECTIVES In this study, the lipopolysaccharide-binding domain (LBD) was identified through machine learning-guided directed evolution, which acts as a functional domain of the anti-lipopolysaccharide factor family of AMPs identified from Marsupenaeus japonicus. METHODS LBDA-D was identified as an output of this algorithm, in which the original LBDMj sequence was the input, and the three-dimensional solution structure of LBDB was determined using nuclear magnetic resonance. Furthermore, our study involved a comprehensive series of experiments, including morphological studies and in vitro and in vivo antibacterial tests. RESULTS The NMR solution structure showed that LBDB possesses a circular extended structure with a disulfide crosslink at the terminus and two 310-helices and exhibits a broad antimicrobial spectrum. In addition, scanning electron microscopy (SEM) and transmission electron microscopy (TEM) showed that LBDB induced the formation of a cluster of bacteria wrapped in a flexible coating that ruptured and consequently killed the bacteria. Finally, coinjection of LBDB, Vibrio alginolyticus and Staphylococcus aureus in vivo improved the survival of M. japonicus, demonstrating the promising therapeutic role of LBDB for treating infectious disease. CONCLUSIONS The findings of this study pave the way for the rational drug design of activity-enhanced peptide antibiotics.
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Affiliation(s)
- Heqian Zhang
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China
| | - Yihan Wang
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China
| | - Yanran Zhu
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China
| | - Pengtao Huang
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China
| | - Qiandi Gao
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China
| | - Xiaojie Li
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China
| | - Zhaoying Chen
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China
| | - Yu Liu
- International Academic Center of Complex Systems, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China
| | - Jiakun Jiang
- Center for Statistics and Data Science, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China
| | - Yuan Gao
- Instrumentation and Service Center for Science and Technology, Beijing Normal University, Zhuhai, Guangdong 519087, China
| | - Jiaquan Huang
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China.
| | - Zhiwei Qin
- Center for Biological Science and Technology, Advanced Institute of Natural Sciences, Beijing Normal University, Zhuhai, Guangdong 519087, China.
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Chen C, Ma B, Wang Y, Cui Q, Yao L, Li Y, Chen B, Feng Y, Tan Z. Structural insight into why S-linked glycosylation cannot adequately mimic the role of natural O-glycosylation. Int J Biol Macromol 2023; 253:126649. [PMID: 37666405 DOI: 10.1016/j.ijbiomac.2023.126649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/21/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
There is an increasing interest in using S-glycosylation as a replacement for the more commonly occurring O-glycosylation, aiming to enhance the resistance of glycans against chemical hydrolysis and enzymatic degradation. However, previous studies have demonstrated that these two types of glycosylation exert distinct effects on protein properties and functions. In order to elucidate the structural basis behind the observed differences, we conducted a systematic and comparative analysis of 6 differently glycosylated forms of a model glycoprotein, CBM, using NMR spectroscopy and molecular dynamic simulations. Our findings revealed that the different stabilizing effects of S- and O-glycosylation could be attributed to altered hydrogen-bonding capability between the glycan and the polypeptide chain, and their diverse impacts on binding affinity could be elucidated by examining the interactions and motion dynamics of glycans in substrate-bound states. Overall, this study underscores the pivotal role of the glycosidic linkage in shaping the function of glycosylation and advises caution when switching glycosylation types in protein glycoengineering.
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Affiliation(s)
- Chao Chen
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao, Shandong 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Ma
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yefei Wang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao, Shandong 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao, Shandong 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lishan Yao
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao, Shandong 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaohao Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Baoquan Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; Shandong Energy Institute, Qingdao, Shandong 266101, China; Qingdao New Energy Shandong Laboratory, Qingdao, Shandong 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhongping Tan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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Chen C, Dong S, Yu Z, Qiao Y, Li J, Ding X, Li R, Lin J, Bayer EA, Liu YJ, Cui Q, Feng Y. Essential autoproteolysis of bacterial anti-σ factor RsgI for transmembrane signal transduction. Sci Adv 2023; 9:eadg4846. [PMID: 37418529 PMCID: PMC10328401 DOI: 10.1126/sciadv.adg4846] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 06/06/2023] [Indexed: 07/09/2023]
Abstract
Autoproteolysis has been discovered to play key roles in various biological processes, but functional autoproteolysis has been rarely reported for transmembrane signaling in prokaryotes. In this study, an autoproteolytic effect was discovered in the conserved periplasmic domain of anti-σ factor RsgIs from Clostridium thermocellum, which was found to transmit extracellular polysaccharide-sensing signals into cells for regulation of the cellulosome system, a polysaccharide-degrading multienzyme complex. Crystal and NMR structures of periplasmic domains from three RsgIs demonstrated that they are different from all known proteins that undergo autoproteolysis. The RsgI-based autocleavage site was located at a conserved Asn-Pro motif between the β1 and β2 strands in the periplasmic domain. This cleavage was demonstrated to be essential for subsequent regulated intramembrane proteolysis to activate the cognate SigI, in a manner similar to that of autoproteolysis-dependent activation of eukaryotic adhesion G protein-coupled receptors. These results indicate the presence of a unique prevalent type of autoproteolytic phenomenon in bacteria for signal transduction.
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Affiliation(s)
- Chao Chen
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaoli Yu
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Yichen Qiao
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Li
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoke Ding
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Renmin Li
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Edward A. Bayer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Life Sciences and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8499000, Israel
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Tan F, Xu J. N-Terminus-Mediated Solution Structure of Dimerization Domain of PRC1. Curr Issues Mol Biol 2022; 44:1626-45. [PMID: 35723369 DOI: 10.3390/cimb44040111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 11/30/2022] Open
Abstract
Microtubule-associated proteins (MAPs) are essential for the accurate division of a cell into two daughter cells. These proteins target specific microtubules to be incorporated into the spindle midzone, which comprises a special array of microtubules that initiate cytokinesis during anaphase. A representative member of the MAPs is Protein Regulator of Cytokinesis 1 (PRC1), which self-multimerizes to cross-link microtubules, the malfunction of which might result in cancerous cells. The importance of PRC1 multimerization makes it a popular target for structural studies. The available crystal structure of PRC1 has low resolution (>3 Å) and accuracy, limiting a better understanding of the structure-related functions of PRC1. Therefore, we used NMR spectroscopy to better determine the structure of the dimerization domain of PRC1. The NMR structure shows that the PRC1 N terminus is crucial to the overall structure integrity, but the crystal structure bespeaks otherwise. We systematically addressed the role of the N terminus by generating a series of mutants in which N-terminal residues methionine (Met1) and arginine (Arg2) were either deleted, extended or substituted with other rationally selected amino acids. Each mutant was subsequently analyzed by NMR spectroscopy or fluorescence thermal shift assays for its structural or thermal stability; we found that N-terminal perturbations indeed affected the overall protein structure and that the solution structure better reflects the conformation of PRC1 under solution conditions. These results reveal that the structure of PRC1 is governed by its N terminus through hydrophobic interactions with other core residues, such hitherto unidentified N-terminal conformations might shed light on the structure−function relationships of PRC1 or other proteins. Therefore, our study is of major importance in terms of identifying a novel structural feature and can further the progress of protein folding and protein engineering.
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Abstract
Methylation of DNA at CpG sites is a major mark for epigenetic regulation, but how transcription factors are influenced by CpG methylation is not well understood. Here, we report the molecular mechanisms of how the TCF (T-cell factor) and GEF (glucose transporter 4 enhancer factor) families of proteins selectively target unmethylated DNA sequences with a C-clamp type zinc finger domain. The structure of the C-clamp domain from human GEF family protein HDBP1 (C-clampHDBP1) in complex with DNA was determined using NMR spectroscopy, which adopts a unique zinc finger fold and selectively binds RCCGG (R = A/G) DNA sequences with an "Arg···Trp-Lys-Lys" DNA recognition motif inserted in the major groove. The CpG base pairs are central to the binding due to multiple hydrogen bonds formed with the backbone carbonyl groups of Trp378 and Lys379, as well as the side chain ε-amino groups of Lys379 and Lys380 from C-clampHDBP1. Consequently, methylation of the CpG dinucleotide almost abolishes the binding. Homology modeling reveals that the C-clamp domain from human TCF1E (C-clampTCF1E) binds DNA through essentially the same mechanism, with a similar "Arg···Arg-Lys-Lys" DNA recognition motif. The substitution of tryptophan by arginine makes C-clampHDBP1 prefer RCCGC DNA sequences. The two signature DNA recognition motifs are invariant in the GEF and TCF families of proteins, respectively, from fly to human. The recognition of the CpG dinucleotide through two consecutive backbone carbonyl groups is the same as that of the CXXC type unmethylated CpG DNA binding domains, suggesting a common mechanism shared by unmethylated CpG binding proteins.
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Affiliation(s)
- Bo Duan
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Dihong Fu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Chaoqun Zhang
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Pengfei Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xianzhi Dong
- Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, and School of Life Sciences, Peking University, Beijing 100871, China
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Ren J, Yao H, Hu W, Perrett S, Gong W, Feng Y. Structural basis for the DNA-binding activity of human ARID4B Tudor domain. J Biol Chem 2021; 296:100506. [PMID: 33675746 PMCID: PMC8038949 DOI: 10.1016/j.jbc.2021.100506] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 11/24/2022] Open
Abstract
Human ARID4A and ARID4B are homologous proteins that are important in controlling gene expression and epigenetic regulation but have distinct functions. Previous studies have shown that the N-terminal domain of ARID4A is an unusual interdigitated double Tudor domain with DNA-binding activity. However, how the Tudor domain of ARID4B differs from that of ARID4A remains unknown. Here, we found that the ARID4B Tudor domain has significantly weaker DNA affinity than the ARID4A Tudor domain despite sharing more than 80% sequence identity. Structure determination and DNA titration analysis indicated that the ARID4B Tudor domain is also an interdigitated double Tudor domain with a DNA-binding surface similar to ARID4A. We identified a residue close to the DNA-binding site of the Tudor domain that differs between ARID4A and ARID4B. The Leu50 in ARID4A is Glu50 in ARID4B, and the latter forms salt bridges with two lysine residues at the DNA-binding surface. This causes a decrease in the strength of positive charge, thus reducing DNA-binding affinity while significantly increasing protein stability. We also found that a C-terminal extension region enhances the DNA-binding affinity of the ARID4B Tudor domain. This C-terminal extension is disordered and contains a positively charged RGR motif, providing an additional DNA-binding site. Finally, sequence and phylogenetic analyses indicated that the residue differences and the presence of the RGR extension region are conserved. These results provide new insight into the functional differences between ARID4A and ARID4B proteins, as well as elucidating the function of the disordered regions in these proteins.
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Affiliation(s)
- Jie Ren
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Hongwei Yao
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Wanhui Hu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Sarah Perrett
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Weibin Gong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Yingang Feng
- University of Chinese Academy of Sciences, Beijing, China; CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.
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Cao B, Xia Z, Hao Z, Liu C, Long D, Fan W, Zhao A. The C-terminal tail of the plant endosomal-type NHXs plays a key role in its function and stability. Plant Sci 2021; 303:110791. [PMID: 33487365 DOI: 10.1016/j.plantsci.2020.110791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Typically, Na+/H+ antiporters (NHXs) possess a conserved N-terminus for cation binding and exchange and a hydrophilic C-terminus for regulating the antiporter activity. Plant endosomal-type NHXs play important roles in protein trafficking, as well as K+ and vesicle pH homeostasis, however the role of the C-terminal tail remains unclear. Here, the function of MnNHX6, an endosomal-type NHX in mulberry, was investigated using heterologous expression in yeast. Functional and localization analyses of C-terminal truncation and mutations in MnNHX6 revealed that the C-terminal conserved region was responsible for the function and stability of the protein and its hydrophobicity, which is a key domain requirement. Nuclear magnetic resonance spectroscopy provided direct structural evidence and yeast two-hybrid screening indicated that this functional domain was also necessary for interaction with sorting nexin 1. Our findings demonstrate that although the C-terminal tail of MnNHX6 is intrinsically disordered, the C-terminal conserved region may be an important part of the external mouth of this transporter, which controls protein function and stability by serving as an inter-molecular cork with a chain mechanism. These findings improve our understanding of the roles of the C-terminal tail of endosomal-type NHXs in plants and the ion transport mechanism of NHX-like antiporters.
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Affiliation(s)
- Boning Cao
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, 400716, China
| | - Zhongqiang Xia
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, 400716, China
| | - Zhanzhang Hao
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, 400716, China
| | - Changying Liu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, 400716, China
| | - Dingpei Long
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, 400716, China
| | - Wei Fan
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, 400716, China
| | - Aichun Zhao
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, 400716, China.
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9
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Yao X, Chen C, Wang Y, Dong S, Liu YJ, Li Y, Cui Z, Gong W, Perrett S, Yao L, Lamed R, Bayer EA, Cui Q, Feng Y. Discovery and mechanism of a pH-dependent dual-binding-site switch in the interaction of a pair of protein modules. Sci Adv 2020; 6:6/43/eabd7182. [PMID: 33097546 PMCID: PMC7608827 DOI: 10.1126/sciadv.abd7182] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/08/2020] [Indexed: 05/23/2023]
Abstract
Many important proteins undergo pH-dependent conformational changes resulting in "on-off" switches for protein function, which are essential for regulation of life processes and have wide application potential. Here, we report a pair of cellulosomal assembly modules, comprising a cohesin and a dockerin from Clostridium acetobutylicum, which interact together following a unique pH-dependent switch between two functional sites rather than on-off states. The two cohesin-binding sites on the dockerin are switched from one to the other at pH 4.8 and 7.5 with a 180° rotation of the bound dockerin. Combined analysis by nuclear magnetic resonance spectroscopy, crystal structure determination, mutagenesis, and isothermal titration calorimetry elucidates the chemical and structural mechanism of the pH-dependent switching of the binding sites. The pH-dependent dual-binding-site switch not only represents an elegant example of biological regulation but also provides a new approach for developing pH-dependent protein devices and biomaterials beyond an on-off switch for biotechnological applications.
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Affiliation(s)
- Xingzhe Yao
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Chen
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Yefei Wang
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Yifei Li
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Zhenling Cui
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weibin Gong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Sarah Perrett
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lishan Yao
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8499000, Israel
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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10
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Yang J, Zhang H, Gong W, Liu Z, Wu H, Hu W, Chen X, Wang L, Wu S, Chen C, Perrett S. S-Glutathionylation of human inducible Hsp70 reveals a regulatory mechanism involving the C-terminal α-helical lid. J Biol Chem 2020; 295:8302-8324. [PMID: 32332101 PMCID: PMC7294093 DOI: 10.1074/jbc.ra119.012372] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/13/2020] [Indexed: 12/23/2022] Open
Abstract
Heat shock protein 70 (Hsp70) proteins are a family of ancient and conserved chaperones. Cysteine modifications have been widely detected among different Hsp70 family members in vivo, but their effects on Hsp70 structure and function are unclear. Here, we treated HeLa cells with diamide, which typically induces disulfide bond formation except in the presence of excess GSH, when glutathionylated cysteines predominate. We show that in these cells, HspA1A (hHsp70) undergoes reversible cysteine modifications, including glutathionylation, potentially at all five cysteine residues. In vitro experiments revealed that modification of cysteines in the nucleotide-binding domain of hHsp70 is prevented by nucleotide binding but that Cys-574 and Cys-603, located in the C-terminal α-helical lid of the substrate-binding domain, can undergo glutathionylation in both the presence and absence of nucleotide. We found that glutathionylation of these cysteine residues results in unfolding of the α-helical lid structure. The unfolded region mimics substrate by binding to and blocking the substrate-binding site, thereby promoting intrinsic ATPase activity and competing with binding of external substrates, including heat shock transcription factor 1 (Hsf1). Thus, post-translational modification can alter the structure and regulate the function of hHsp70.
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Affiliation(s)
- Jie Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China.,University of the Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China .,University of the Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Weibin Gong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Zhenyan Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Huiwen Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China.,University of the Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Wanhui Hu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China.,University of the Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Xinxin Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China.,University of the Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Lei Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China.,University of the Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Si Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China.,University of the Chinese Academy of Sciences, Shijingshan District, Beijing, China
| | - Chang Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China .,University of the Chinese Academy of Sciences, Shijingshan District, Beijing, China.,Beijing Institute for Brain Disorders, Youanmen, Beijing, China
| | - Sarah Perrett
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing, China .,University of the Chinese Academy of Sciences, Shijingshan District, Beijing, China
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11
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Wei Z, Chen C, Liu YJ, Dong S, Li J, Qi K, Liu S, Ding X, Ortiz de Ora L, Muñoz-Gutiérrez I, Li Y, Yao H, Lamed R, Bayer EA, Cui Q, Feng Y. Alternative σI/anti-σI factors represent a unique form of bacterial σ/anti-σ complex. Nucleic Acids Res 2019; 47:5988-5997. [PMID: 31106374 PMCID: PMC6582324 DOI: 10.1093/nar/gkz355] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/21/2019] [Accepted: 04/26/2019] [Indexed: 12/18/2022] Open
Abstract
The σ70 family alternative σI factors and their cognate anti-σI factors are widespread in Clostridia and Bacilli and play a role in heat stress response, virulence, and polysaccharide sensing. Multiple σI/anti-σI factors exist in some lignocellulolytic clostridial species, specifically for regulation of components of a multienzyme complex, termed the cellulosome. The σI and anti-σI factors are unique, because the C-terminal domain of σI (SigIC) and the N-terminal inhibitory domain of anti-σI (RsgIN) lack homology to known proteins. Here, we report structure and interaction studies of a pair of σI and anti-σI factors, SigI1 and RsgI1, from the cellulosome-producing bacterium, Clostridium thermocellum. In contrast to other known anti-σ factors that have N-terminal helical structures, RsgIN has a β-barrel structure. Unlike other anti-σ factors that bind both σ2 and σ4 domains of the σ factors, RsgIN binds SigIC specifically. Structural analysis showed that SigIC contains a positively charged surface region that recognizes the promoter -35 region, and the synergistic interactions among multiple interfacial residues result in the specificity displayed by different σI/anti-σI pairs. We suggest that the σI/anti-σI factors represent a distinctive mode of σ/anti-σ complex formation, which provides the structural basis for understanding the molecular mechanism of the intricate σI/anti-σI system.
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Affiliation(s)
- Zhen Wei
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Chen
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Jie Li
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuan Qi
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiyue Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoke Ding
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Lizett Ortiz de Ora
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Iván Muñoz-Gutiérrez
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Yifei Li
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Hongwei Yao
- High-Field Nuclear Magnetic Resonance Center, Xiamen University, 422 South Siming Road, Xiamen 361005, China
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- To whom correspondence should be addressed. Tel: +86 532 80662706; Fax: +86 532 80662707;
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12
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Yao X, Liu YJ, Cui Q, Feng Y. Solution structure of a unicellular microalgae-derived translationally controlled tumor protein revealed both conserved features and structural diversity. Arch Biochem Biophys 2019; 665:23-29. [PMID: 30797749 DOI: 10.1016/j.abb.2019.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/16/2019] [Accepted: 02/18/2019] [Indexed: 10/27/2022]
Abstract
Translationally controlled tumor proteins (TCTPs) are eukaryote-conserved multifunctional proteins, but their primary functions are not well understood yet. Study on TCTP from unicellular species may provide insight into the primary function of the TCTP family. Bioinformatic analysis indicated that the TCTP from Nannochloropsis oceanica (NoTCTP), a model unicellular microalga for biodiesel and polyunsaturated fatty acid production, has low sequence homology to other structure-known TCTPs and two TCTP signature patterns are not detected in NoTCTP. Hence, we determined the solution structure of NoTCTP. The overall structure of NoTCTP, including a long flexible loop, a β-barrel subdomain, and a helical subdomain, is generally similar to other TCTP structures. NoTCTP has a eukaryote-conserved surface for the binding of eukaryotic elongation factor 1B, confirming that TCTP is involved in protein synthesis, which is one of the primary functions of TCTP. Additionally, NoTCTP has distinct features different from other TCTPs. NoTCTP structure lacks a short α-helix which exists in all other known TCTP structures. The helical subdomain and some loops of NoTCTP also have distinct conformations among the TCTP family proteins. Therefore, our study on NoTCTP revealed not only conserved structural features but also the structural diversity of TCTP family proteins.
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Affiliation(s)
- Xingzhe Yao
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
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13
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Duan B, Ding P, Hughes TR, Navarre WW, Liu J, Xia B. How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome. Nucleic Acids Res 2018; 46:10514-10529. [PMID: 30252102 PMCID: PMC6212790 DOI: 10.1093/nar/gky836] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/28/2018] [Accepted: 09/18/2018] [Indexed: 12/11/2022] Open
Abstract
Bacterial xenogeneic silencers play important roles in bacterial evolution by recognizing and inhibiting expression from foreign genes acquired through horizontal gene transfer, thereby buffering against potential fitness consequences of their misregulated expression. Here, the detailed DNA binding properties of Rok, a xenogeneic silencer in Bacillus subtilis, was studied using protein binding microarray, and the solution structure of its C-terminal DNA binding domain was determined in complex with DNA. The C-terminal domain of Rok adopts a typical winged helix fold, with a novel DNA recognition mechanism different from other winged helix proteins or xenogeneic silencers. Rok binds the DNA minor groove by forming hydrogen bonds to bases through N154, T156 at the N-terminal of α3 helix and R174 of wing W1, assisted by four lysine residues interacting electrostatically with DNA backbone phosphate groups. These structural features endow Rok with preference towards DNA sequences harboring AACTA, TACTA, and flexible multiple TpA steps, while rigid A-tracts are disfavored. Correspondingly, the Bacillus genomes containing Rok are rich in A-tracts and show a dramatic underrepresentation of AACTA and TACTA, which are significantly enriched in Rok binding regions. These observations suggest that the xenogeneic silencing protein and its resident genome may have evolved cooperatively.
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Affiliation(s)
- Bo Duan
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing 100871, China
| | - Pengfei Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing 100871, China
| | - Timothy R Hughes
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - William Wiley Navarre
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Jun Liu
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University, Beijing 100871, China
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14
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Zhang W, Zhao C, Hu Y, Jin C. Solution structure of the N-terminal domain of proteasome lid subunit Rpn5. Biochem Biophys Res Commun 2018; 504:225-230. [PMID: 30177392 DOI: 10.1016/j.bbrc.2018.08.159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 08/26/2018] [Indexed: 11/29/2022]
Abstract
The 26S proteasome is the major protein degradation machinery in living cells. The Rpn5 protein is one scaffolding subunit in the lid subcomplex of the 19S regulatory particle in the proteasome holoenzyme. Herein we report the solution structure of the N-terminal domain (NTD) of yeast Rpn5 at high resolution by NMR spectroscopy. The results show that Rpn5 NTD adopts α-solenoid-like fold in right-handed superhelical configuration formed by a number of α-helices. Structural comparisons with currently available cryo-EM structures reveal local structural differences in the first three helices between yeast and human Rpn5. The results further highlight the conformational flexibility in three possible protein interaction sites. Moreover, the structures of the NTD show large variations among different PCI-containing Rpn subunits. Our current results provide atomic-level structural basis for further investigations of protein-protein interactions and the proteasome assembly pathway.
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Affiliation(s)
- Wenbo Zhang
- College of Life Sciences, Peking University, Beijing 100871, China; Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
| | - Cong Zhao
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
| | - Yunfei Hu
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China.
| | - Changwen Jin
- College of Life Sciences, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China.
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15
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Gong W, Hu W, Xu L, Wu H, Wu S, Zhang H, Wang J, Jones GW, Perrett S. The C-terminal GGAP motif of Hsp70 mediates substrate recognition and stress response in yeast. J Biol Chem 2018; 293:17663-17675. [PMID: 30228181 DOI: 10.1074/jbc.ra118.002691] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 08/30/2018] [Indexed: 01/16/2023] Open
Abstract
The allosteric coupling of the highly conserved nucleotide- and substrate-binding domains of Hsp70 has been studied intensively. In contrast, the role of the disordered, highly variable C-terminal region of Hsp70 remains unclear. In many eukaryotic Hsp70s, the extreme C-terminal EEVD motif binds to the tetratricopeptide-repeat domains of Hsp70 co-chaperones. Here, we discovered that the TVEEVD sequence of Saccharomyces cerevisiae cytoplasmic Hsp70 (Ssa1) functions as a SUMO-interacting motif. A second C-terminal motif of ∼15 amino acids between the α-helical lid and the extreme C terminus, previously identified in bacterial and eukaryotic organellar Hsp70s, is known to enhance chaperone function by transiently interacting with folding clients. Using structural analysis, interaction studies, fibril formation assays, and in vivo functional assays, we investigated the individual contributions of the α-helical bundle and the C-terminal disordered region of Ssa1 in the inhibition of fibril formation of the prion protein Ure2. Our results revealed that although the α-helical bundle of the Ssa1 substrate-binding domain (SBDα) does not directly bind to Ure2, the SBDα enhances the ability of Hsp70 to inhibit fibril formation. We found that a 20-residue C-terminal motif in Ssa1, containing GGAP and GGAP-like tetrapeptide repeats, can directly bind to Ure2, the Hsp40 co-chaperone Ydj1, and α-synuclein, but not to the SUMO-like protein SMT3 or BSA. Deletion or substitution of the Ssa1 GGAP motif impaired yeast cell tolerance to temperature and cell-wall damage stress. This study highlights that the C-terminal GGAP motif of Hsp70 is important for substrate recognition and mediation of the heat shock response.
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Affiliation(s)
- Weibin Gong
- From the National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wanhui Hu
- From the National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Linan Xu
- Department of Biology, Maynooth University, Maynooth, W23 W6R7, Kildare, Ireland
| | - Huiwen Wu
- From the National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Si Wu
- From the National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Zhang
- From the National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jinfeng Wang
- From the National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Gary W Jones
- Department of Biology, Maynooth University, Maynooth, W23 W6R7, Kildare, Ireland.
| | - Sarah Perrett
- From the National Laboratory of Biomacromolecules, Chinese Academy of Sciences Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
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16
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Zhou T, Yao X, Wang J, Feng Y. Solution structure of an archaeal DUF61 family protein SSO0941 encoded by a gene in the operon of box C/D RNA protein complexes. J Struct Biol 2018. [PMID: 29526782 DOI: 10.1016/j.jsb.2018.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Domain of unknown function 61 (DUF61) family proteins widely exist in archaea and the genes of DUF61 proteins in crenarchaea are in an operon containing two genes of box C/D RNA protein complexes. Here we report the solution NMR structure of DUF61 family member protein SSO0941, from the hyperthermophilic archaeon Sulfolobus solfataricus. SSO0941 has a rigid core structure and flexible N- and C-terminal regions as well as a negatively-charged independent C-terminal helix. The core structure consists of N- and C-terminal subdomains, in which the C-terminal subdomain shows significant structural similarity with several nucleic acid binding proteins. The structure of SSO0941 is the first representative structure of DUF61 family proteins.
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Affiliation(s)
- Tao Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xingzhe Yao
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Jinfeng Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China; CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
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17
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Klein BJ, Wang X, Cui G, Yuan C, Botuyan MV, Lin K, Lu Y, Wang X, Zhao Y, Bruns CJ, Mer G, Shi X, Kutateladze TG. PHF20 Readers Link Methylation of Histone H3K4 and p53 with H4K16 Acetylation. Cell Rep 2017; 17:1158-1170. [PMID: 27760318 DOI: 10.1016/j.celrep.2016.09.056] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 09/05/2016] [Accepted: 09/16/2016] [Indexed: 01/06/2023] Open
Abstract
PHF20 is a core component of the lysine acetyltransferase complex MOF (male absent on the first)-NSL (non-specific lethal) that generates the major epigenetic mark H4K16ac and is necessary for transcriptional regulation and DNA repair. The role of PHF20 in the complex remains elusive. Here, we report on functional coupling between methylation readers in PHF20. We show that the plant homeodomain (PHD) finger of PHF20 recognizes dimethylated lysine 4 of histone H3 (H3K4me2) and represents an example of a native reader that selects for this modification. Biochemical and structural analyses help to explain this selectivity and the preference of Tudor2, another reader in PHF20, for dimethylated p53. Binding of the PHD finger to H3K4me2 is required for histone acetylation, accumulation of PHF20 at target genes, and transcriptional activation. Together, our findings establish a unique PHF20-mediated link between MOF histone acetyltransferase (HAT), p53, and H3K4me2, and suggest a model for rapid spreading of H4K16ac-enriched open chromatin.
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Affiliation(s)
- Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Xiaoyan Wang
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Faculty of Medicine, Ludwig Maximilian University of Munich, Munich 80336, Germany
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Chao Yuan
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaolu Wang
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yue Zhao
- Department of General, Visceral and Tumor Surgery, University Clinic Cologne, Cologne 50931, Germany
| | - Christiane J Bruns
- Faculty of Medicine, Ludwig Maximilian University of Munich, Munich 80336, Germany; Department of General, Visceral and Tumor Surgery, University Clinic Cologne, Cologne 50931, Germany
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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18
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Yu XC, Yang C, Ding J, Niu X, Hu Y, Jin C. Characterizations of the Interactions between Escherichia coli Periplasmic Chaperone HdeA and Its Native Substrates during Acid Stress. Biochemistry 2017; 56:5748-5757. [PMID: 29016106 DOI: 10.1021/acs.biochem.7b00724] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bacterial acid-resistant chaperone HdeA is a "conditionally disordered" protein that functions at low pH when it undergoes a transition from a well-folded dimer to an unfolded monomer. The dimer dissociation and unfolding processes result in exposure of hydrophobic surfaces that allows binding to a broad range of client proteins. To fully elucidate the chaperone mechanism of HdeA, it is crucial to understand how the activated HdeA interacts with its native substrates during acid stress. Herein, we present a nuclear magnetic resonance study of the pH-dependent HdeA-substrate interactions. Our results show that the activation of HdeA is not only induced by acidification but also regulated by the presence of unfolded substrates. The variable extent of unfolding of substrates differentially regulates the HdeA-substrate interaction, and the binding further affects the HdeA conformation. Finally, we show that HdeA binds its substrates heterogeneously, and the "amphiphilic" model for HdeA-substrate interaction is discussed.
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Affiliation(s)
- Xing-Chi Yu
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Chengfeng Yang
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Jienv Ding
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Yunfei Hu
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
| | - Changwen Jin
- College of Chemistry and Molecular Engineering, ‡Beijing Nuclear Magnetic Resonance Center, §College of Life Sciences, and ∥Beijing National Laboratory for Molecular Sciences, Peking University , Beijing 100871, China
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19
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Chaffey PK, Guan X, Chen C, Ruan Y, Wang X, Tran AH, Koelsch TN, Cui Q, Feng Y, Tan Z. Structural Insight into the Stabilizing Effect of O-Glycosylation. Biochemistry 2017; 56:2897-2906. [DOI: 10.1021/acs.biochem.7b00195] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Patrick K. Chaffey
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Xiaoyang Guan
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Chao Chen
- Shandong
Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory
of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Yuan Ruan
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Xinfeng Wang
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Amy H. Tran
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Theo N. Koelsch
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
| | - Qiu Cui
- Shandong
Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory
of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Yingang Feng
- Shandong
Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory
of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Zhongping Tan
- Department
of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado 80303, United States
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20
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Abstract
Mitophagy is a fundamental process that determines mitochondrial quality and homeostasis. Several mitophagy receptors, including the newly identified FUNDC1, mediate selective removal of damaged or superfluous mitochondria through their specific interaction with LC3. However, the precise mechanism by which this interaction is regulated to initiate mitophagy is not understood. Here, we report the solution structure of LC3 in complex with a peptide containing the FUNDC1 LC3-interacting region (LIR) motif. The structure reveals a noncanonical LC3-LIR binding conformation, in which the third LIR residue (Val20) is also inserted into the hydrophobic pocket of LC3, together with the conserved residues Tyr18 and Leu21. This enables Tyr18 to be positioned near Asp19 of LC3, and thus phosphorylation of Tyr18 significantly weakens the binding affinity due to electrostatic repulsion. Functional analysis revealed that mitochondrial targeting of the LIR-containing cytosolic portion of FUNDC1 is necessary and sufficient to initiate mitophagy when Tyr18 is unphosphorylated, even in the absence of mitochondrial fragmentation. Thus, we demonstrated that phosphorylation of Tyr18 of FUNDC1 serves as a molecular switch for mitophagy. This may represent a novel target for therapeutic intervention.
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Affiliation(s)
- Yao Kuang
- a Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University , Beijing , China
| | - Kaili Ma
- b State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University , Tianjin , China
| | - Changqian Zhou
- b State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University , Tianjin , China
| | - Pengfei Ding
- a Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University , Beijing , China
| | - Yushan Zhu
- b State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University , Tianjin , China
| | - Quan Chen
- b State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, College of Life Sciences, Nankai University , Tianjin , China.,c State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences , Beijing , China
| | - Bin Xia
- a Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, School of Life Sciences, Peking University , Beijing , China
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21
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Wu H, Wang C, Gong W, Wang J, Xuan J, Perrett S, Feng Y. The C-terminal region of human eukaryotic elongation factor 1Bδ. J Biomol NMR 2016; 64:181-187. [PMID: 26762120 DOI: 10.1007/s10858-016-0012-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/06/2016] [Indexed: 06/05/2023]
Affiliation(s)
- Huiwen Wu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chen Wang
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, 266101, Shandong, China
- Shandong Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, 266101, Shandong, China
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, 266101, Shandong, China
- Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Weibin Gong
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinsong Xuan
- Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Sarah Perrett
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yingang Feng
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, 266101, Shandong, China.
- Shandong Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, 266101, Shandong, China.
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, 266101, Shandong, China.
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22
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Ding J, Yang C, Niu X, Hu Y, Jin C. HdeB chaperone activity is coupled to its intrinsic dynamic properties. Sci Rep 2015; 5:16856. [PMID: 26593705 PMCID: PMC4655364 DOI: 10.1038/srep16856] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 10/21/2015] [Indexed: 11/09/2022] Open
Abstract
Enteric bacteria encounter extreme acidity when passing through hosts' stomach. Since the bacterial periplasmic space quickly equilibrates with outer environment, an efficient acid resistance mechanism is essential in preventing irreversible protein denaturation/aggregation and maintaining bacteria viability. HdeB, along with its homolog HdeA, was identified as a periplasmic acid-resistant chaperone. Both proteins exist as homodimers and share similar monomeric structures under neutral pH, while showing different dimeric packing interfaces. Previous investigations show that HdeA functions through an acid-induced dimer-to-monomer transition and partial unfolding at low pH (pH 2-3), resulting in exposure of hydrophobic surfaces that bind substrate proteins. In contrast, HdeB appears to have a much higher optimal activation pH (pH 4-5), under which condition the protein maintains a well-folded dimer and the mechanism for its chaperone activity remains elusive. Herein, we present an NMR study of HdeB to investigate its dynamic properties. Our results reveal that HdeB undergoes significant micro- to milli-second timescale conformational exchanges at neutral to near-neutral pH, under the later condition it exhibits optimal activity. The current study indicates that HdeB activation is coupled to its intrinsic dynamics instead of structural changes, and therefore its functional mechanism is apparently different from HdeA.
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Affiliation(s)
- Jienv Ding
- College of Life Sciences, Peking University, Beijing 100871, China.,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
| | - Chengfeng Yang
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
| | - Yunfei Hu
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
| | - Changwen Jin
- College of Life Sciences, Peking University, Beijing 100871, China.,College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China.,Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
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23
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Abstract
Three-dimensional structures of proteins in solution can be calculated on the basis of conformational restraints derived from NMR measurements. This chapter gives an overview of the computational methods for NMR protein structure analysis highlighting recent automated methods for the assignment of NMR spectra, the collection of conformational restraints, and the structure calculation.
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24
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Hu C, Yu C, Liu Y, Hou X, Liu X, Hu Y, Jin C. A Hybrid Mechanism for the Synechocystis Arsenate Reductase Revealed by Structural Snapshots during Arsenate Reduction. J Biol Chem 2015. [PMID: 26224634 DOI: 10.1074/jbc.m115.659896] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Evolution of enzymes plays a crucial role in obtaining new biological functions for all life forms. Arsenate reductases (ArsC) are several families of arsenic detoxification enzymes that reduce arsenate to arsenite, which can subsequently be extruded from cells by specific transporters. Among these, the Synechocystis ArsC (SynArsC) is structurally homologous to the well characterized thioredoxin (Trx)-coupled ArsC family but requires the glutaredoxin (Grx) system for its reactivation, therefore classified as a unique Trx/Grx-hybrid family. The detailed catalytic mechanism of SynArsC is unclear and how the "hybrid" mechanism evolved remains enigmatic. Herein, we report the molecular mechanism of SynArsC by biochemical and structural studies. Our work demonstrates that arsenate reduction is carried out via an intramolecular thiol-disulfide cascade similar to the Trx-coupled family, whereas the enzyme reactivation step is diverted to the coupling of the glutathione-Grx pathway due to the local structural difference. The current results support the hypothesis that SynArsC is likely a molecular fossil representing an intermediate stage during the evolution of the Trx-coupled ArsC family from the low molecular weight protein phosphotyrosine phosphatase (LMW-PTPase) family.
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Affiliation(s)
- Cuiyun Hu
- From the College of Chemistry and Molecular Engineering, Beijing Nuclear Magnetic Resonance Center
| | - Caifang Yu
- From the College of Chemistry and Molecular Engineering, Beijing Nuclear Magnetic Resonance Center
| | - Yanhua Liu
- From the College of Chemistry and Molecular Engineering
| | - Xianhui Hou
- From the College of Chemistry and Molecular Engineering, Beijing Nuclear Magnetic Resonance Center
| | - Xiaoyun Liu
- From the College of Chemistry and Molecular Engineering
| | - Yunfei Hu
- From the College of Chemistry and Molecular Engineering, Beijing Nuclear Magnetic Resonance Center,
| | - Changwen Jin
- From the College of Chemistry and Molecular Engineering, Beijing Nuclear Magnetic Resonance Center, College of Life Sciences, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
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25
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Ding P, McFarland KA, Jin S, Tong G, Duan B, Yang A, Hughes TR, Liu J, Dove SL, Navarre WW, Xia B. A Novel AT-Rich DNA Recognition Mechanism for Bacterial Xenogeneic Silencer MvaT. PLoS Pathog 2015; 11:e1004967. [PMID: 26068099 PMCID: PMC4466236 DOI: 10.1371/journal.ppat.1004967] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 05/21/2015] [Indexed: 11/18/2022] Open
Abstract
Bacterial xenogeneic silencing proteins selectively bind to and silence expression from many AT rich regions of the chromosome. They serve as master regulators of horizontally acquired DNA, including a large number of virulence genes. To date, three distinct families of xenogeneic silencers have been identified: H-NS of Proteobacteria, Lsr2 of the Actinomycetes, and MvaT of Pseudomonas sp. Although H-NS and Lsr2 family proteins are structurally different, they all recognize the AT-rich DNA minor groove through a common AT-hook-like motif, which is absent in the MvaT family. Thus, the DNA binding mechanism of MvaT has not been determined. Here, we report the characteristics of DNA sequences targeted by MvaT with protein binding microarrays, which indicates that MvaT prefers binding flexible DNA sequences with multiple TpA steps. We demonstrate that there are clear differences in sequence preferences between MvaT and the other two xenogeneic silencer families. We also determined the structure of the DNA-binding domain of MvaT in complex with a high affinity DNA dodecamer using solution NMR. This is the first experimental structure of a xenogeneic silencer in complex with DNA, which reveals that MvaT recognizes the AT-rich DNA both through base readout by an "AT-pincer" motif inserted into the minor groove and through shape readout by multiple lysine side chains interacting with the DNA sugar-phosphate backbone. Mutations of key MvaT residues for DNA binding confirm their importance with both in vitro and in vivo assays. This novel DNA binding mode enables MvaT to better tolerate GC-base pair interruptions in the binding site and less prefer A tract DNA when compared to H-NS and Lsr2. Comparison of MvaT with other bacterial xenogeneic silencers provides a clear picture that nature has evolved unique solutions for different bacterial genera to distinguish foreign from self DNA.
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Affiliation(s)
- Pengfei Ding
- Beijing Nuclear Magnetic Resonance Center, School of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Kirsty A. McFarland
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shujuan Jin
- Beijing Nuclear Magnetic Resonance Center, School of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Grace Tong
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Bo Duan
- Beijing Nuclear Magnetic Resonance Center, School of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Ally Yang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Timothy R. Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Simon L. Dove
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (SLD); (WWN); (BX)
| | - William Wiley Navarre
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (SLD); (WWN); (BX)
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, School of Life Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- * E-mail: (SLD); (WWN); (BX)
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26
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Buchner L, Güntert P. Systematic evaluation of combined automated NOE assignment and structure calculation with CYANA. J Biomol NMR 2015; 62:81-95. [PMID: 25796507 DOI: 10.1007/s10858-015-9921-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/16/2015] [Indexed: 05/07/2023]
Abstract
The automated assignment of NOESY cross peaks has become a fundamental technique for NMR protein structure analysis. A widely used algorithm for this purpose is implemented in the program CYANA. It has been used for a large number of structure determinations of proteins in solution but a systematic evaluation of its performance has not yet been reported. In this paper we systematically analyze the reliability of combined automated NOESY assignment and structure calculation with CYANA under a variety of conditions on the basis of the experimental NMR data sets of ten proteins. To evaluate the robustness of the algorithm, the original high-quality experimental data sets were modified in different ways to simulate the effect of data imperfections, i.e. incomplete or erroneous chemical shift assignments, missing NOESY cross peaks, inaccurate peak positions, inaccurate peak intensities, lower dimensionality NOESY spectra, and higher tolerances for the matching of chemical shifts and peak positions. The results show that the algorithm is remarkably robust with regard to imperfections of the NOESY peak lists and the chemical shift tolerances but susceptible to lacking or erroneous resonance assignments, in particular for nuclei that are involved in many NOESY cross peaks.
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Affiliation(s)
- Lena Buchner
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
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27
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Wei H, Wang L, Ren X, Yu W, Lin J, Jin C, Xia B. Structural and functional characterization of tumor suppressors TIG3 and H-REV107. FEBS Lett 2015; 589:1179-86. [PMID: 25871522 DOI: 10.1016/j.febslet.2015.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/16/2015] [Accepted: 04/01/2015] [Indexed: 11/30/2022]
Abstract
H-REV107-like family proteins TIG3 and H-REV107 are class II tumor suppressors. Here we report that the C-terminal domains (CTDs) of TIG3 and H-REV107 can induce HeLa cell death independently. The N-terminal domain (NTD) of TIG3 enhances the cell death inducing ability of CTD, while NTD of H-REV107 plays an inhibitory role. The solution structure of TIG3 NTD is very similar to that of H-REV107 in overall fold. However, the CTD binding regions on NTD are different between TIG3 and H-REV107, which may explain their functional difference. As a result, the flexible main loop of H-REV107, but not that of TIG3, is critical for its NTD to modulate its CTD in inducing cell death.
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Affiliation(s)
- Hejia Wei
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking University, Beijing 100871, China
| | - Lei Wang
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaobai Ren
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenyu Yu
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking University, Beijing 100871, China
| | - Jian Lin
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China; School of Life Sciences, Peking University, Beijing 100871, China; College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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Abstract
The regulatory particle (RP) of the 26 S proteasome functions in preparing polyubiquitinated substrates for degradation. The lid complex of the RP contains an Rpn8-Rpn11 heterodimer surrounded by a horseshoe-shaped scaffold formed by six proteasome-COP9/CSN-initiation factor (PCI)-containing subunits. The PCI domains are essential for lid assembly, whereas the detailed molecular mechanisms remain elusive. Recent cryo-EM studies at near-atomic resolution provided invaluable information on the RP architecture in different functional states. Nevertheless, atomic resolution structural information on the RP is still limited, and deeper understanding of RP assembly mechanism requires further studies on the structures and interactions of individual subunits or subcomplexes. Herein we report the high-resolution NMR structures of the PCI-containing subunit Rpn9 from Saccharomyces cerevisiae. The 45-kDa protein contains an all-helical N-terminal domain and a C-terminal PCI domain linked via a semiflexible hinge. The N-terminal domain mediates interaction with the ubiquitin receptor Rpn10, whereas the PCI domain mediates interaction with the neighboring PCI subunit Rpn5. The Rpn9-Rpn5 interface highlights two structural motifs on the winged helix module forming a hydrophobic center surrounded by ionic pairs, which is a common pattern for all PCI-PCI interactions in the lid. The results suggest that divergence in surface composition among different PCI pairs may contribute to the modulation of lid assembly.
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Affiliation(s)
- Yunfei Hu
- From the Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering
| | - Yujie Wu
- From the Beijing Nuclear Magnetic Resonance Center, College of Life Sciences, and
| | - Qianwen Li
- From the Beijing Nuclear Magnetic Resonance Center, College of Life Sciences, and
| | - Wenbo Zhang
- From the Beijing Nuclear Magnetic Resonance Center, College of Life Sciences, and
| | - Changwen Jin
- From the Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, College of Life Sciences, and Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
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29
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Tong Q, Cui G, Botuyan MV, Rothbart SB, Hayashi R, Musselman CA, Singh N, Appella E, Strahl BD, Mer G, Kutateladze TG. Structural plasticity of methyllysine recognition by the tandem tudor domain of 53BP1. Structure 2015; 23:312-21. [PMID: 25579814 DOI: 10.1016/j.str.2014.11.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 11/29/2022]
Abstract
p53 is dynamically regulated through various posttranslational modifications (PTMs), which differentially modulate its function and stability. The dimethylated marks p53K370me2 and p53K382me2 are associated with p53 activation or stabilization and both are recognized by the tandem Tudor domain (TTD) of 53BP1, a p53 cofactor. Here we detail the molecular mechanisms for the recognition of p53K370me2 and p53K382me2 by 53BP1. The solution structures of TTD in complex with the p53K370me2 and p53K382me2 peptides show a remarkable plasticity of 53BP1 in accommodating these diverse dimethyllysine-containing sequences. We demonstrate that dimeric TTDs are capable of interacting with the two PTMs on a single p53K370me2K382me2 peptide, greatly strengthening the 53BP1-p53 interaction. Analysis of binding affinities of TTD toward methylated p53 and histones reveals strong preference of 53BP1 for p53K382me2, H4K20me2, and H3K36me2 and suggests a possible role of multivalent contacts of 53BP1 in p53 targeting to and accumulation at the sites of DNA damage.
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Affiliation(s)
- Qiong Tong
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Scott B Rothbart
- Department of Biochemistry and Biophysics and the Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Ryo Hayashi
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Catherine A Musselman
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Namit Singh
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ettore Appella
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics and the Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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30
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Chen C, Cui Z, Xiao Y, Cui Q, Smith SP, Lamed R, Bayer EA, Feng Y. Revisiting the NMR solution structure of the Cel48S type-I dockerin module from Clostridium thermocellum reveals a cohesin-primed conformation. J Struct Biol 2014; 188:188-93. [PMID: 25270376 DOI: 10.1016/j.jsb.2014.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 09/20/2014] [Accepted: 09/22/2014] [Indexed: 11/29/2022]
Abstract
Dockerin modules of the cellulosomal enzyme subunits play an important role in the assembly of the cellulosome by binding tenaciously to cohesin modules of the scaffoldin subunit. A previously reported NMR-derived solution structure of the type-I dockerin module from Cel48S of Clostridium thermocellum, which utilized two-dimensional homonuclear (1)H-(1)H NOESY and three-dimensional (15)N-edited NOESY distance restraints, displayed substantial conformational differences from subsequent structures of dockerin modules in complex with their cognate cohesin modules, raising the question whether the source of the observed differences resulted from cohesin-induced structural rearrangements. Here, we determined the solution structure of the Cel48S type-I dockerin based on (15)N- and (13)C-edited NOESY-derived distance restraints. The structure adopted a fold similar to X-ray crystal structures of dockerin modules in complex with their cohesin partners. A unique cis-peptide bond between Leu-65 and Pro-66 in the Cel48S type-I dockerin module was also identified in the present structure. Our structural analysis of the Cel48S type-I dockerin module indicates that it does not undergo appreciable cohesin-induced structural alterations but rather assumes an inherent calcium-dependent cohesin-primed conformation.
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Affiliation(s)
- Chao Chen
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenling Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Xiao
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China; Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, Shandong 266101, China
| | - Steven P Smith
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Edward A Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China.
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31
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Ye Q, Hu Y, Jin C. Conformational dynamics of Escherichia coli flavodoxins in apo- and holo-states by solution NMR spectroscopy. PLoS One 2014; 9:e103936. [PMID: 25093851 PMCID: PMC4122359 DOI: 10.1371/journal.pone.0103936] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 07/08/2014] [Indexed: 11/23/2022] Open
Abstract
Flavodoxins are a family of small FMN-binding proteins that commonly exist in prokaryotes. They utilize a non-covalently bound FMN molecule to act as the redox center during the electron transfer processes in various important biological pathways. Although extensive investigations were performed, detailed molecular mechanisms of cofactor binding and electron transfer remain elusive. Herein we report the solution NMR studies on Escherichia coli flavodoxins FldA and YqcA, belonging to the long-chain and short-chain flavodoxin subfamilies respectively. Our structural studies demonstrate that both proteins show the typical flavodoxin fold, with extensive conformational exchanges observed near the FMN binding pocket in their apo-forms. Cofactor binding significantly stabilizes both proteins as revealed by the extension of secondary structures in the holo-forms, and the overall rigidity shown by the backbone dynamics data. However, the 50 s loops of both proteins in the holo-form still show conformational exchanges on the µs-ms timescales, which appears to be a common feature in the flavodoxin family, and might play an important role in structural fine-tuning during the electron transfer reactions.
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Affiliation(s)
- Qian Ye
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, China
- College of Life Sciences, Peking University, Beijing, China
| | - Yunfei Hu
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- * E-mail: (YF); (CJ)
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing, China
- College of Life Sciences, Peking University, Beijing, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- * E-mail: (YF); (CJ)
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32
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Feng Y, Song X, Lin J, Xuan J, Cui Q, Wang J. Structure determination of archaea-specific ribosomal protein L46a reveals a novel protein fold. Biochem Biophys Res Commun 2014; 450:67-72. [PMID: 24875358 DOI: 10.1016/j.bbrc.2014.05.077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 05/16/2014] [Indexed: 01/21/2023]
Abstract
Three archaea-specific ribosomal proteins recently identified show no sequence homology with other known proteins. Here we determined the structure of L46a, the most conserved one among the three proteins, from Sulfolobus solfataricus P2 using NMR spectroscopy. The structure presents a twisted β-sheet formed by the N-terminal part and two helices at the C-terminus. The L46a structure has a positively charged surface which is conserved in the L46a protein family and is the potential rRNA-binding site. Searching homologous structures in Protein Data Bank revealed that the structure of L46a represents a novel protein fold. The backbone dynamics identified by NMR relaxation experiments reveal significant flexibility at the rRNA binding surface. The potential position of L46a on the ribosome was proposed by fitting the structure into a previous electron microscopy map of the ribosomal 50S subunit, which indicated that L46a contacts to domain I of 23S rRNA near a multifunctional ribosomal protein L7ae.
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Affiliation(s)
- Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.
| | - Xiaxia Song
- Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Jinzhong Lin
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinsong Xuan
- Department of Biological Science and Engineering, School of Chemical and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Qiu Cui
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Jinfeng Wang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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33
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Li G, Qu L, Ma S, Wu Y, Jin C, Zheng X. Structure determination of human Fas apoptosis inhibitory molecule and identification of the critical residues linking the interdomain interaction to the anti-apoptotic activity. ACTA ACUST UNITED AC 2014; 70:1812-22. [DOI: 10.1107/s1399004714004854] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 03/03/2014] [Indexed: 11/10/2022]
Abstract
Fas apoptosis inhibitory molecule (FAIM) is a highly conserved anti-apoptotic protein which plays important roles in cells. There are two isoforms of FAIM, of which the short isoform FAIM-S is broadly expressed in all tissues, whereas the long isoform FAIM-L is exclusively expressed in the nervous system. No structure of human FAIM has been reported to date and the detailed molecular mechanisms underlying the anti-apoptotic function of FAIM remain unknown. Here, the crystal structure of the human FAIM-S N-terminal domain (NTD) and the NMR solution structure of the human FAIM-S C-terminal domain (CTD) were determined. The structures revealed that the NTD and CTD adopt a similar protein fold containing eight antiparallel β-strands which form two sheets. Both structural and biochemical analyses implied that the NTD exists as a dimer and the CTD as a monomer and that they can interact with each other. Several critical residues were identified to be involved in this interaction. Moreover, mutations of these critical residues also interfered in the anti-apoptotic activity of FAIM-S. Thus, the structural and functional data presented here will provide insight into the anti-apoptotic mechanism of FAIM-S.
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Gu J, Feng Y, Feng X, Sun C, Lei L, Ding W, Niu F, Jiao L, Yang M, Li Y, Liu X, Song J, Cui Z, Han D, Du C, Yang Y, Ouyang S, Liu ZJ, Han W. Structural and biochemical characterization reveals LysGH15 as an unprecedented "EF-hand-like" calcium-binding phage lysin. PLoS Pathog 2014; 10:e1004109. [PMID: 24831957 PMCID: PMC4022735 DOI: 10.1371/journal.ppat.1004109] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/25/2014] [Indexed: 11/18/2022] Open
Abstract
The lysin LysGH15, which is derived from the staphylococcal phage GH15, demonstrates a wide lytic spectrum and strong lytic activity against methicillin-resistant Staphylococcus aureus (MRSA). Here, we find that the lytic activity of the full-length LysGH15 and its CHAP domain is dependent on calcium ions. To elucidate the molecular mechanism, the structures of three individual domains of LysGH15 were determined. Unexpectedly, the crystal structure of the LysGH15 CHAP domain reveals an “EF-hand-like” calcium-binding site near the Cys-His-Glu-Asn quartet active site groove. To date, the calcium-binding site in the LysGH15 CHAP domain is unique among homologous proteins, and it represents the first reported calcium-binding site in the CHAP family. More importantly, the calcium ion plays an important role as a switch that modulates the CHAP domain between the active and inactive states. Structure-guided mutagenesis of the amidase-2 domain reveals that both the zinc ion and E282 are required in catalysis and enable us to propose a catalytic mechanism. Nuclear magnetic resonance (NMR) spectroscopy and titration-guided mutagenesis identify residues (e.g., N404, Y406, G407, and T408) in the SH3b domain that are involved in the interactions with the substrate. To the best of our knowledge, our results constitute the first structural information on the biochemical features of a staphylococcal phage lysin and represent a pivotal step forward in understanding this type of lysin. The staphylococcal phage lysin LysGH15 demonstrates great potential against methicillin-resistant Staphylococcus aureus (MRSA). Here, we report that the lytic activity of LysGH15 and its CHAP domain is dependent on calcium ions. To elucidate the molecular mechanism, we determined the structures of three individual LysGH15 domains using X-ray crystallography or nuclear magnetic resonance (NMR). The crystal structure unexpectedly reveals an “EF-hand-like” calcium-binding site near the Cys-His-Glu-Asn quartet active site groove in the LysGH15 CHAP domain. Furthermore, the calcium ion plays an important role as a switch that modulates the lytic activity of the CHAP domain. Additionally, structure-guided mutagenesis also confirms that both E282 and the zinc ion play an important role in maintaining the lytic activity of the LysGH15 amidase-2 domain. Moreover, the NMR structure and titration-guided mutagenesis identify residues in the LysGH15 SH3b domain that are involved in the interactions with the substrate. The structure of LysGH15 is the first determined lysin structure from a staphylococcal phage, and these results represent a pivotal step forward in understanding this type of lysin.
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Affiliation(s)
- Jingmin Gu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Xin Feng
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Changjiang Sun
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Liancheng Lei
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Wei Ding
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fengfeng Niu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Lianying Jiao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Mei Yang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yue Li
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xiaohe Liu
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jun Song
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Ziyin Cui
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Dong Han
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Chongtao Du
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yongjun Yang
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Songying Ouyang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (SO); (ZJL); (WH)
| | - Zhi-Jie Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail: (SO); (ZJL); (WH)
| | - Wenyu Han
- Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
- * E-mail: (SO); (ZJL); (WH)
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Jiao L, Ouyang S, Shaw N, Song G, Feng Y, Niu F, Qiu W, Zhu H, Hung LW, Zuo X, Eleonora Shtykova V, Zhu P, Dong YH, Xu R, Liu ZJ. Mechanism of the Rpn13-induced activation of Uch37. Protein Cell 2014; 5:616-30. [PMID: 24752541 PMCID: PMC4130924 DOI: 10.1007/s13238-014-0046-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 02/25/2014] [Indexed: 01/22/2023] Open
Abstract
Uch37 is a de-ubiquitinating enzyme that is activated by Rpn13 and involved in the proteasomal degradation of proteins. The full-length Uch37 was shown to exhibit low iso-peptidase activity and is thought to be auto-inhibited. Structural comparisons revealed that within a homo-dimer of Uch37, each of the catalytic domains was blocking the other's ubiquitin (Ub)-binding site. This blockage likely prevented Ub from entering the active site of Uch37 and might form the basis of auto-inhibition. To understand the mode of auto-inhibition clearly and shed light on the activation mechanism of Uch37 by Rpn13, we investigated the Uch37-Rpn13 complex using a combination of mutagenesis, biochemical, NMR, and small-angle X-ray scattering (SAXS) techniques. Our results also proved that Uch37 oligomerized in solution and had very low activity against the fluorogenic substrate ubiquitin-7-amino-4-methylcoumarin (Ub-AMC) of de-ubiquitinating enzymes. Uch37Δ(Hb,Hc,KEKE), a truncation removal of the C-terminal extension region (residues 256-329) converted oligomeric Uch37 into a monomeric form that exhibited iso-peptidase activity comparable to that of a truncation-containing the Uch37 catalytic domain only. We also demonstrated that Rpn13C (Rpn13 residues 270-407) could disrupt the oligomerization of Uch37 by sequestering Uch37 and forming a Uch37-Rpn13 complex. Uch37 was activated in such a complex, exhibiting 12-fold-higher activity than Uch37 alone. Time-resolved SAXS (TR-SAXS) and FRET experiments supported the proposed mode of auto-inhibition and the activation mechanism of Uch37 by Rpn13. Rpn13 activated Uch37 by forming a 1:1 stoichiometric complex in which the active site of Uch37 was accessible to Ub.
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Affiliation(s)
- Lianying Jiao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Songying Ouyang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Neil Shaw
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Gaojie Song
- iHuman Institute, ShanghaiTech University, Shanghai, 201210 China
| | - Yingang Feng
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Fengfeng Niu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Weicheng Qiu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Hongtao Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Li-Wei Hung
- Physics Division, Los Alamos National Laboratory, Los Alamos, NM 87545 USA
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439 USA
| | - V. Eleonora Shtykova
- Institute of Crystallography, Russian Academy of Sciences, 59 Leninsky Pr., 117333 Moscow, Russian Federation
| | - Ping Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yu-Hui Dong
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, 100049 China
| | - Ruxiang Xu
- Department of Nerosurgery, The Military General Hospital of Beijing PLA, Beijing, 100700 China
| | - Zhi-Jie Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
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36
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Abstract
Retinoblastoma-binding protein 1 (RBBP1) is a tumor and leukemia suppressor that binds both methylated histone tails and DNA. Our previous studies indicated that RBBP1 possesses a Tudor domain, which cannot bind histone marks. In order to clarify the function of the Tudor domain, the solution structure of the RBBP1 Tudor domain was determined by NMR and is presented here. Although the proteins are unrelated, the RBBP1 Tudor domain forms an interdigitated double Tudor structure similar to the Tudor domain of JMJD2A, which is an epigenetic mark reader. This indicates the functional diversity of Tudor domains. The RBBP1 Tudor domain structure has a significant area of positively charged surface, which reveals a capability of the RBBP1 Tudor domain to bind nucleic acids. NMR titration and isothermal titration calorimetry experiments indicate that the RBBP1 Tudor domain binds both double- and single-stranded DNA with an affinity of 10-100 μM; no apparent DNA sequence specificity was detected. The DNA binding mode and key interaction residues were analyzed in detail based on a model structure of the Tudor domain-dsDNA complex, built by HADDOCK docking using the NMR data. Electrostatic interactions mediate the binding of the Tudor domain with DNA, which is consistent with NMR experiments performed at high salt concentration. The DNA-binding residues are conserved in Tudor domains of the RBBP1 protein family, resulting in conservation of the DNA-binding function in the RBBP1 Tudor domains. Our results provide further insights into the structure and function of RBBP1.
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Affiliation(s)
- Weibin Gong
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China and
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37
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Ouyang B, Wang L, Wan S, Luo Y, Wang L, Lin J, Xia B. Solution structure of monomeric human FAM96A. J Biomol NMR 2013; 56:387-392. [PMID: 23793605 DOI: 10.1007/s10858-013-9746-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 05/14/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Bingjie Ouyang
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
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Wu X, Subramaniam S, Case DA, Wu KW, Brooks BR. Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps. J Struct Biol 2013; 183:429-440. [PMID: 23876978 DOI: 10.1016/j.jsb.2013.07.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 07/11/2013] [Accepted: 07/12/2013] [Indexed: 11/30/2022]
Abstract
We present a map-restrained self-guided Langevin dynamics (MapSGLD) simulation method for efficient targeted conformational search. The targeted conformational search represents simulations under restraints defined by experimental observations and/or by user specified structural requirements. Through map-restraints, this method provides an efficient way to maintain substructures and to set structure targets during conformational searching. With an enhanced conformational searching ability of self-guided Langevin dynamics, this approach is suitable for simulating large-scale conformational changes, such as the formation of macromolecular assemblies and transitions between different conformational states. Using several examples, we illustrate the application of this method in flexible fitting of atomic structures into density maps derived from cryo-electron microscopy.
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Affiliation(s)
- Xiongwu Wu
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA.
| | - Sriram Subramaniam
- Laboratory of Cell Biology, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - David A Case
- BioMaPS Institute and Dept. of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Katherine W Wu
- Thomas Jefferson High School for Science and Technology, Alexandria, VA 22312, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
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Cui G, Park S, Badeaux AI, Kim D, Lee J, Thompson JR, Yan F, Kaneko S, Yuan Z, Botuyan MV, Bedford MT, Cheng JQ, Mer G. PHF20 is an effector protein of p53 double lysine methylation that stabilizes and activates p53. Nat Struct Mol Biol 2012; 19:916-24. [PMID: 22864287 DOI: 10.1038/nsmb.2353] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Accepted: 07/06/2012] [Indexed: 12/26/2022]
Abstract
PHF20 is a multidomain protein and subunit of a lysine acetyltransferase complex that acetylates histone H4 and p53 but whose function is unclear. Using biochemical, biophysical and cellular approaches, we determined that PHF20 is a direct regulator of p53. A Tudor domain in PHF20 recognized p53 dimethylated at Lys370 or Lys382 and a homodimeric form of this Tudor domain could associate with the two dimethylated sites on p53 with enhanced affinity, indicating a multivalent interaction. Association with PHF20 promotes stabilization and activation of p53 by diminishing Mdm2-mediated p53 ubiquitylation and degradation. PHF20 contributes to upregulation of p53 in response to DNA damage, and ectopic expression of PHF20 in different cell lines leads to phenotypic changes that are hallmarks of p53 activation. Overall our work establishes that PHF20 functions as an effector of p53 methylation that stabilizes and activates p53.
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Gong W, Zhou T, Mo J, Perrett S, Wang J, Feng Y. Structural insight into recognition of methylated histone tails by retinoblastoma-binding protein 1. J Biol Chem 2012; 287:8531-40. [PMID: 22247551 DOI: 10.1074/jbc.m111.299149] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Retinoblastoma-binding protein 1 (RBBP1), also named AT-rich interaction domain containing 4A (ARID4A), is a tumor and leukemia suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. Although the involvement in epigenetic regulation is proposed to involve its chromobarrel and/or Tudor domains because of their potential binding to methylated histone tails, the structures of these domains and their interactions with methylated histone tails are still uncharacterized. In this work, we first found that RBBP1 contains five domains by bioinformatics analysis. Three of the five domains, i.e. chromobarrel, Tudor, and PWWP domains, are Royal Family domains, which potentially bind to methylated histone tails. We further purified these domains and characterized their interaction with methylated histone tails by NMR titration experiments. Among the three Royal Family domains, only the chromobarrel domain could recognize trimethylated H4K20 (with an affinity of ∼3 mm), as well as recognizing trimethylated H3K9, H3K27, and H3K36 (with lower affinities). The affinity could be further enhanced up to 15-fold by the presence of DNA. The structure of the chromobarrel domain of RBBP1 determined by NMR spectroscopy has an aromatic cage. Mutagenesis analysis identified four aromatic residues of the cage as the key residues for methylated lysine recognition. Our studies indicate that the chromobarrel domain of RBBP1 is responsible for recognizing methylated histone tails in chromatin remodeling and epigenetic regulation, which presents a significant advance in our understanding of the mechanism and relationship between RBBP1-related gene suppression and epigenetic regulation.
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Affiliation(s)
- Weibin Gong
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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41
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Abstract
In solution or solid-state, determining the three-dimensional structure of biomolecules by Nuclear -Magnetic Resonance (NMR) normally requires the collection of distance information. The interpretation of the spectra containing this distance information is a critical step in an NMR structure determination. In this chapter, we present the Ambiguous Restraints for Iterative Assignment (ARIA) program for automated cross-peak assignment and determination of macromolecular structure from solution and solid-state NMR experiments. While the program was initially designed for the assignment of nuclear Overhauser effect (NOE) resonances, it has been extended to the interpretation of magic-angle spinning (MAS) solid-state NMR data. This chapter first details the concepts and procedures carried out by the program. Then, we describe both the general strategy for structure determination with ARIA 2.3 and practical aspects of the technique. ARIA 2.3 includes all recent developments. such as an extended integration of the Collaborative Computing Project for the NMR community (CCPN), the incorporation of the log-harmonic distance restraint potential and an automated treatment of symmetric oligomers.
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Affiliation(s)
- Benjamin Bardiaux
- NMR-supported Structural Biology, Leibnitz-Institutfür Molekulare Pharmakologie (FMP), Berlin, Germany.
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42
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Abstract
LCI, a 47-residue cationic antimicrobial peptide (AMP) found in Bacillus subtilis, is one of the main effective components that have strong antimicrobial activity against Xanthomonas campestris pv Oryzea and Pseudomonas solanacearum PE1, etc. To provide insight into the activity of the peptide, we used nuclear magnetic resonance spectroscopy to determine the structure of recombinant LCI. The solution structure of LCI has a novel topology, containing a four-strand antiparallel β-sheet as the dominant secondary structure. It is the first structure of the LCI protein family. Different from any known β-structure AMPs, LCI contains no disulfide bridge or circular structure, suggesting that LCI is also a novel β-structure AMP.
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Affiliation(s)
- Weibin Gong
- The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China 100871
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43
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Abstract
Around half of all protein structures solved nowadays using solution-state nuclear magnetic resonance (NMR) spectroscopy have been because of automated data analysis. The pervasiveness of computational approaches in general hides, however, a more nuanced view in which the full variety and richness of the field appears. This review is structured around a comparison of methods associated with three NMR observables: classical nuclear Overhauser effect (NOE) constraint gathering in contrast with more recent chemical shift and residual dipole coupling (RDC) based protocols. In each case, the emphasis is placed on the latest research, covering mainly the past 5 years. By describing both general concepts and representative programs, the objective is to map out a field in which--through the very profusion of approaches--it is all too easy to lose one's bearings.
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Hu Y, Zhang X, Shi Y, Zhou Y, Zhang W, Su XD, Xia B, Zhao J, Jin C. Structures of Anabaena calcium-binding protein CcbP: insights into Ca2+ signaling during heterocyst differentiation. J Biol Chem 2011; 286:12381-8. [PMID: 21330362 DOI: 10.1074/jbc.m110.201186] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Ca2+-binding proteins play pivotal roles in both eukaryotic and prokaryotic cells. CcbP from cyanobacterium Anabaena sp. strain PCC 7120 is a major Ca2+-binding protein involved in heterocyst differentiation, a process that forms specialized nitrogen-fixing cells. The three-dimensional structures of both Ca2+-free and Ca2+-bound forms of CcbP are essential for elucidating the Ca2+-signaling mechanism. However, CcbP shares low sequence identity with proteins of known structures, and its Ca2+-binding sites remain unknown. Here, we report the solution structures of CcbP in both Ca2+-free and Ca2+-bound forms determined by nuclear magnetic resonance spectroscopy. CcbP adopts an overall new fold and contains two Ca2+-binding sites with distinct Ca2+-binding abilities. Mutation of Asp38 at the stronger Ca2+-binding site of CcbP abolished its ability to regulate heterocyst formation in vivo. Surprisingly, the β-barrel subdomain of CcbP, which does not participate in Ca2+-binding, topologically resembles the Src homology 3 (SH3) domain and might act as a protein-protein interaction module. Our results provide the structural basis of the unique Ca2+ signaling mechanism during heterocyst differentiation.
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Affiliation(s)
- Yunfei Hu
- Beijing Nuclear Magnetic Resonance Center, State Key Laboratory of Plant and Protein Engineering, College of Life Sciences, Peking University, Beijing, China
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Chen Y, Rai R, Zhou ZR, Kanoh J, Ribeyre C, Yang Y, Zheng H, Damay P, Wang F, Tsujii H, Hiraoka Y, Shore D, Hu HY, Chang S, Lei M. A conserved motif within RAP1 has diversified roles in telomere protection and regulation in different organisms. Nat Struct Mol Biol 2011; 18:213-21. [PMID: 21217703 DOI: 10.1038/nsmb.1974] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 11/04/2010] [Indexed: 12/29/2022]
Abstract
Repressor activator protein 1 (RAP1) is the most highly conserved telomere protein. It is involved in protecting chromosome ends in fission yeast and promoting gene silencing in Saccharomyces cerevisiae, whereas it represses homology-directed recombination at telomeres in mammals. To understand how RAP1 has such diverse functions at telomeres, we solved the crystal or solution structures of the RAP1 C-terminal (RCT) domains of RAP1 from multiple organisms in complex with their respective protein-binding partners. Our analysis establishes RAP1(RCT) as an evolutionarily conserved protein-protein interaction module. In mammalian and fission yeast cells, this module interacts with TRF2 and Taz1, respectively, targeting RAP1 to chromosome ends for telomere protection. In contrast, S. cerevisiae RAP1 uses its RCT domain to recruit Sir3 to telomeres to mediate gene silencing. Together, our results show that, depending on the organism, the evolutionarily conserved RAP1 RCT motif has diverse functional roles at telomeres.
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Affiliation(s)
- Yong Chen
- Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Cui G, Benirschke RC, Tuan HF, Juranić N, Macura S, Botuyan MV, Mer G. Structural basis of ubiquitin recognition by translesion synthesis DNA polymerase ι. Biochemistry 2010; 49:10198-207. [PMID: 21049971 DOI: 10.1021/bi101303t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cells have evolved mutagenic bypass mechanisms that prevent stalling of the replication machinery at DNA lesions. This process, translesion DNA synthesis (TLS), involves switching from high-fidelity DNA polymerases to specialized DNA polymerases that replicate through a variety of DNA lesions. In eukaryotes, polymerase switching during TLS is regulated by the DNA damage-triggered monoubiquitylation of PCNA. How the switch operates is unknown, but all TLS polymerases of the so-called Y-family possess PCNA and ubiquitin-binding domains that are important for their function. To gain insight into the structural mechanisms underlying the regulation of TLS by ubiquitylation, we have probed the interaction of ubiquitin with a conserved ubiquitin-binding motif (UBM2) of Y-family polymerase Polι. Using NMR spectroscopy, we have determined the structure of a complex of human Polι UBM2 and ubiquitin, revealing a novel ubiquitin recognition fold consisting of two α-helices separated by a central trans-proline residue conserved in all UBMs. We show that, different from the majority of ubiquitin complexes characterized to date, ubiquitin residue Ile44 only plays a modest role in the association of ubiquitin with Polι UBM2. Instead, binding of UBM2 is centered on the recognition of Leu8 in ubiquitin, which is essential for the interaction.
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Affiliation(s)
- Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, United States
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47
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Affiliation(s)
- Xuan Shao
- Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
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Hu J, Cui G, Li C, Liu C, Shang E, Lai L, Jin C, Wang J, Xia B. Structure and novel functional mechanism of Drosophila SNF in sex-lethal splicing. PLoS One 2009; 4:e6890. [PMID: 19727396 PMCID: PMC2731243 DOI: 10.1371/journal.pone.0006890] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 07/29/2009] [Indexed: 11/18/2022] Open
Abstract
Sans-fille (SNF) is the Drosophila homologue of mammalian general splicing factors U1A and U2B'', and it is essential in Drosophila sex determination. We found that, besides its ability to bind U1 snRNA, SNF can also bind polyuridine RNA tracts flanking the male-specific exon of the master switch gene Sex-lethal (Sxl) pre-mRNA specifically, similar to Sex-lethal protein (SXL). The polyuridine RNA binding enables SNF directly inhibit Sxl exon 3 splicing, as the dominant negative mutant SNF(1621) binds U1 snRNA but not polyuridine RNA. Unlike U1A, both RNA recognition motifs (RRMs) of SNF can recognize polyuridine RNA tracts independently, even though SNF and U1A share very high sequence identity and overall structure similarity. As SNF RRM1 tends to self-associate on the opposite side of the RNA binding surface, it is possible for SNF to bridge the formation of super-complexes between two introns flanking Sxl exon 3 or between a intron and U1 snRNP, which serves the molecular basis for SNF to directly regulate Sxl splicing. Taken together, a new functional model for SNF in Drosophila sex determination is proposed. The key of the new model is that SXL and SNF function similarly in promoting Sxl male-specific exon skipping with SNF being an auxiliary or backup to SXL, and it is the combined dose of SXL and SNF governs Drosophila sex determination.
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Affiliation(s)
- Jicheng Hu
- Beijing Nuclear Magnetic Resonance Center, Beijing, People's Republic of China
- College of Life Sciences, Peking University, Beijing, People's Republic of China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China
| | - Gaofeng Cui
- Beijing Nuclear Magnetic Resonance Center, Beijing, People's Republic of China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China
| | - Congmin Li
- Beijing Nuclear Magnetic Resonance Center, Beijing, People's Republic of China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China
| | - Cong Liu
- College of Life Sciences, Peking University, Beijing, People's Republic of China
| | - Erchang Shang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China
| | - Luhua Lai
- College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, Beijing, People's Republic of China
- College of Life Sciences, Peking University, Beijing, People's Republic of China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China
| | - Jiwu Wang
- Allele Biotechnology & Pharmaceuticals, Inc., San Diego, California, United States of America
- * E-mail: (BX); (JW)
| | - Bin Xia
- Beijing Nuclear Magnetic Resonance Center, Beijing, People's Republic of China
- College of Life Sciences, Peking University, Beijing, People's Republic of China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, People's Republic of China
- * E-mail: (BX); (JW)
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Xu Y, Amero CD, Pulukkunat DK, Gopalan V, Foster MP. Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-RNA interactions. J Mol Biol 2009; 393:1043-55. [PMID: 19733182 DOI: 10.1016/j.jmb.2009.08.068] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 08/28/2009] [Accepted: 08/30/2009] [Indexed: 01/05/2023]
Abstract
Ribonuclease P (RNase P) is a ribonucleoprotein (RNP) enzyme that catalyzes the Mg(2+)-dependent 5' maturation of precursor tRNAs. In all domains of life, it is a ribozyme: the RNase P RNA (RPR) component has been demonstrated to be responsible for catalysis. However, the number of RNase P protein subunits (RPPs) varies from 1 in bacteria to 9 or 10 in eukarya. The archaeal RPR is associated with at least 4 RPPs, which function in pairs (RPP21-RPP29 and RPP30-POP5). We used solution NMR spectroscopy to determine the three-dimensional structure of the protein-protein complex comprising Pyrococcus furiosus RPP21 and RPP29. We found that the protein-protein interaction is characterized by coupled folding of secondary structural elements that participate in interface formation. In addition to detailing the intermolecular contacts that stabilize this 30-kDa binary complex, the structure identifies surfaces rich in conserved basic residues likely vital for recognition of the RPR and/or precursor tRNA. Furthermore, enzymatic footprinting experiments allowed us to localize the RPP21-RPP29 complex to the specificity domain of the RPR. These findings provide valuable new insights into mechanisms of RNP assembly and serve as important steps towards a three-dimensional model of this ancient RNP enzyme.
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Affiliation(s)
- Yiren Xu
- Ohio State Biochemistry Program, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
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Wang J, Zuo X, Yu P, Xu H, Starich MR, Tiede DM, Shapiro BA, Schwieters CD, Wang YX. A method for helical RNA global structure determination in solution using small-angle x-ray scattering and NMR measurements. J Mol Biol 2009; 393:717-34. [PMID: 19666030 DOI: 10.1016/j.jmb.2009.08.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Revised: 08/04/2009] [Accepted: 08/04/2009] [Indexed: 10/20/2022]
Abstract
We report a "top-down" method that uses mainly duplexes' global orientations and overall molecular dimension and shape restraints, which were extracted from experimental NMR and small-angle X-ray scattering data, respectively, to determine global architectures of RNA molecules consisting of mostly A-form-like duplexes. The method is implemented in the G2G (from global measurement to global structure) toolkit of programs. We demonstrate the efficiency and accuracy of the method by determining the global structure of a 71-nt RNA using experimental data. The backbone root-mean-square deviation of the ensemble of the calculated global structures relative to the X-ray crystal structure is 3.0+/-0.3 A using the experimental data and is only 2.5+/-0.2 A for the three duplexes that were orientation restrained during the calculation. The global structure simplifies interpretation of multidimensional nuclear Overhauser spectra for high-resolution structure determination. The potential general application of the method for RNA structure determination is discussed.
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Affiliation(s)
- Jinbu Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, National Cancer Institute at Frederick/NIH, Frederick, MD 21702, USA
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