101
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Kronfel CM, Kuzin AP, Forouhar F, Biswas A, Su M, Lew S, Seetharaman J, Xiao R, Everett JK, Ma LC, Acton TB, Montelione GT, Hunt JF, Paul CEC, Dragomani TM, Boutaghou MN, Cole RB, Riml C, Alvey RM, Bryant DA, Schluchter WM. Structural and biochemical characterization of the bilin lyase CpcS from Thermosynechococcus elongatus. Biochemistry 2013; 52:8663-76. [PMID: 24215428 DOI: 10.1021/bi401192z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyanobacterial phycobiliproteins have evolved to capture light energy over most of the visible spectrum due to their bilin chromophores, which are linear tetrapyrroles that have been covalently attached by enzymes called bilin lyases. We report here the crystal structure of a bilin lyase of the CpcS family from Thermosynechococcus elongatus (TeCpcS-III). TeCpcS-III is a 10-stranded β barrel with two alpha helices and belongs to the lipocalin structural family. TeCpcS-III catalyzes both cognate as well as noncognate bilin attachment to a variety of phycobiliprotein subunits. TeCpcS-III ligates phycocyanobilin, phycoerythrobilin, and phytochromobilin to the alpha and beta subunits of allophycocyanin and to the beta subunit of phycocyanin at the Cys82-equivalent position in all cases. The active form of TeCpcS-III is a dimer, which is consistent with the structure observed in the crystal. With the use of the UnaG protein and its association with bilirubin as a guide, a model for the association between the native substrate, phycocyanobilin, and TeCpcS was produced.
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Affiliation(s)
- Christina M Kronfel
- Department of Biological Sciences, University of New Orleans , New Orleans, LA 70148, United States
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102
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Meng L, Forouhar F, Thieker D, Gao Z, Ramiah A, Moniz H, Xiang Y, Seetharaman J, Milaninia S, Su M, Bridger R, Veillon L, Azadi P, Kornhaber G, Wells L, Montelione GT, Woods RJ, Tong L, Moremen KW. Enzymatic basis for N-glycan sialylation: structure of rat α2,6-sialyltransferase (ST6GAL1) reveals conserved and unique features for glycan sialylation. J Biol Chem 2013; 288:34680-98. [PMID: 24155237 DOI: 10.1074/jbc.m113.519041] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Glycan structures on glycoproteins and glycolipids play critical roles in biological recognition, targeting, and modulation of functions in animal systems. Many classes of glycan structures are capped with terminal sialic acid residues, which contribute to biological functions by either forming or masking glycan recognition sites on the cell surface or secreted glycoconjugates. Sialylated glycans are synthesized in mammals by a single conserved family of sialyltransferases that have diverse linkage and acceptor specificities. We examined the enzymatic basis for glycan sialylation in animal systems by determining the crystal structures of rat ST6GAL1, an enzyme that creates terminal α2,6-sialic acid linkages on complex-type N-glycans, at 2.4 Å resolution. Crystals were obtained from enzyme preparations generated in mammalian cells. The resulting structure revealed an overall protein fold broadly resembling the previously determined structure of pig ST3GAL1, including a CMP-sialic acid-binding site assembled from conserved sialylmotif sequence elements. Significant differences in structure and disulfide bonding patterns were found outside the sialylmotif sequences, including differences in residues predicted to interact with the glycan acceptor. Computational substrate docking and molecular dynamics simulations were performed to predict and evaluate the CMP-sialic acid donor and glycan acceptor interactions, and the results were compared with kinetic analysis of active site mutants. Comparisons of the structure with pig ST3GAL1 and a bacterial sialyltransferase revealed a similar positioning of donor, acceptor, and catalytic residues that provide a common structural framework for catalysis by the mammalian and bacterial sialyltransferases.
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Affiliation(s)
- Lu Meng
- From the Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
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103
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Neklesa TK, Noblin DJ, Kuzin A, Lew S, Seetharaman J, Acton TB, Kornhaber G, Xiao R, Montelione GT, Tong L, Crews CM. A bidirectional system for the dynamic small molecule control of intracellular fusion proteins. ACS Chem Biol 2013; 8:2293-2300. [PMID: 23978068 DOI: 10.1021/cb400569k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Small molecule control of intracellular protein levels allows temporal and dose-dependent regulation of protein function. Recently, we developed a method to degrade proteins fused to a mutant dehalogenase (HaloTag2) using small molecule hydrophobic tags (HyTs). Here, we introduce a complementary method to stabilize the same HaloTag2 fusion proteins, resulting in a unified system allowing bidirectional control of cellular protein levels in a temporal and dose-dependent manner. From a small molecule screen, we identified N-(3,5-dichloro-2-ethoxybenzyl)-2H-tetrazol-5-amine as a nanomolar HALoTag2 Stabilizer (HALTS1) that reduces the Hsp70:HaloTag2 interaction, thereby preventing HaloTag2 ubiquitination. Finally, we demonstrate the utility of the HyT/HALTS system in probing the physiological role of therapeutic targets by modulating HaloTag2-fused oncogenic H-Ras, which resulted in either the cessation (HyT) or acceleration (HALTS) of cellular transformation. In sum, we present a general platform to study protein function, whereby any protein of interest fused to HaloTag2 can be either degraded 10-fold or stabilized 5-fold using two corresponding compounds.
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Affiliation(s)
- Taavi K. Neklesa
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, 219
Prospect Street, New Haven, Connecticut 06511, United States
| | - Devin J. Noblin
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, 219
Prospect Street, New Haven, Connecticut 06511, United States
| | - Alexander Kuzin
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Scott Lew
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Jayaraman Seetharaman
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Thomas B. Acton
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Gregory Kornhaber
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Rong Xiao
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Gaetano T. Montelione
- Center
for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Department
of Biochemistry and Molecular Biology, Robert Wood Johnson
Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Liang Tong
- Department
of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Craig M. Crews
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, 219
Prospect Street, New Haven, Connecticut 06511, United States
- Department
of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06511, United States
- Department
of Pharmacology, Yale University, 333 Cedar Street, New Haven, Connecticut 06511, United States
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104
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Abstract
Biomolecular NMR structures are now routinely used in biology, chemistry, and bioinformatics. Methods and metrics for assessing the accuracy and precision of protein NMR structures are beginning to be standardized across the biological NMR community. These include both knowledge-based assessment metrics, parameterized from the database of protein structures, and model versus data assessment metrics. On line servers are available that provide comprehensive protein structure quality assessment reports, and efforts are in progress by the world-wide Protein Data Bank (wwPDB) to develop a biomolecular NMR structure quality assessment pipeline as part of the structure deposition process. These quality assessment metrics and standards will aid NMR spectroscopists in determining more accurate structures, and increase the value and utility of these structures for the broad scientific community.
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Affiliation(s)
- Antonio Rosato
- Magnetic Resonance Center and Department of Chemistry, University of Florence, 50019 Sesto Fiorentino, Italy
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105
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Xu SY, Kuzin AP, Seetharaman J, Gutjahr A, Chan SH, Chen Y, Xiao R, Acton TB, Montelione GT, Tong L. Structure determination and biochemical characterization of a putative HNH endonuclease from Geobacter metallireducens GS-15. PLoS One 2013; 8:e72114. [PMID: 24039739 PMCID: PMC3765158 DOI: 10.1371/journal.pone.0072114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [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: 06/03/2013] [Accepted: 07/12/2013] [Indexed: 01/07/2023] Open
Abstract
The crystal structure of a putative HNH endonuclease, Gmet_0936 protein from Geobacter metallireducens GS-15, has been determined at 2.6 Å resolution using single-wavelength anomalous dispersion method. The structure contains a two-stranded anti-parallel β-sheet that are surrounded by two helices on each face, and reveals a Zn ion bound in each monomer, coordinated by residues Cys38, Cys41, Cys73, and Cys76, which likely plays an important structural role in stabilizing the overall conformation. Structural homologs of Gmet_0936 include Hpy99I endonuclease, phage T4 endonuclease VII, and other HNH endonucleases, with these enzymes sharing 15-20% amino acid sequence identity. An overlay of Gmet_0936 and Hpy99I structures shows that most of the secondary structure elements, catalytic residues as well as the zinc binding site (zinc ribbon) are conserved. However, Gmet_0936 lacks the N-terminal domain of Hpy99I, which mediates DNA binding as well as dimerization. Purified Gmet_0936 forms dimers in solution and a dimer of the protein is observed in the crystal, but with a different mode of dimerization as compared to Hpy99I. Gmet_0936 and its N77H variant show a weak DNA binding activity in a DNA mobility shift assay and a weak Mn²⁺-dependent nicking activity on supercoiled plasmids in low pH buffers. The preferred substrate appears to be acid and heat-treated DNA with AP sites, suggesting Gmet_0936 may be a DNA repair enzyme.
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Affiliation(s)
- Shuang-yong Xu
- New England Biolabs, Inc. Research Department, Ipswich, Massachusetts, United States of America
- * E-mail: (SX); (LT)
| | - Alexandre P. Kuzin
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York, United States of America
| | - Jayaraman Seetharaman
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York, United States of America
| | - Alice Gutjahr
- New England Biolabs, Inc. Research Department, Ipswich, Massachusetts, United States of America
| | - Siu-Hong Chan
- New England Biolabs, Inc. Research Department, Ipswich, Massachusetts, United States of America
| | - Yang Chen
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York, United States of America
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Department of Biochemistry, Robert Wood Johnson Medical School, Northeast Structural Genomics Consortium, Piscataway, New Jersey, United States of America
| | - Thomas B. Acton
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Department of Biochemistry, Robert Wood Johnson Medical School, Northeast Structural Genomics Consortium, Piscataway, New Jersey, United States of America
| | - Gaetano T. Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Department of Biochemistry, Robert Wood Johnson Medical School, Northeast Structural Genomics Consortium, Piscataway, New Jersey, United States of America
| | - Liang Tong
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York, United States of America
- * E-mail: (SX); (LT)
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106
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Pulavarti SVSRK, He Y, Feldmann EA, Eletsky A, Acton TB, Xiao R, Everett JK, Montelione GT, Kennedy MA, Szyperski T. Solution NMR structures provide first structural coverage of the large protein domain family PF08369 and complementary structural coverage of dark operative protochlorophyllide oxidoreductase complexes. J Struct Funct Genomics 2013; 14:119-126. [PMID: 23963952 PMCID: PMC3982801 DOI: 10.1007/s10969-013-9159-5] [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] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Accepted: 07/16/2013] [Indexed: 06/02/2023]
Abstract
High-quality NMR structures of the C-terminal domain comprising residues 484-537 of the 537-residue protein Bacterial chlorophyll subunit B (BchB) from Chlorobium tepidum and residues 9-61 of 61-residue Asr4154 from Nostoc sp. (strain PCC 7120) exhibit a mixed α/β fold comprised of three α-helices and a small β-sheet packed against second α-helix. These two proteins share 29% sequence similarity and their structures are globally quite similar. The structures of BchB(484-537) and Asr4154(9-61) are the first representative structures for the large protein family (Pfam) PF08369, a family of unknown function currently containing 610 members in bacteria and eukaryotes. Furthermore, BchB(484-537) complements the structural coverage of the dark-operating protochlorophyllide oxidoreductase.
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Affiliation(s)
- Surya VSRK Pulavarti
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, NY 14260, USA
| | - Yunfen He
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, NY 14260, USA
| | - Erik A. Feldmann
- Department of Chemistry and Biochemistry, Miami University, and Northeast Structural Genomics Consortium, Oxford, OH 45056, USA
| | - Alexander Eletsky
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, NY 14260, USA
| | - Thomas B. Acton
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Rong Xiao
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - John K. Everett
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Gaetano T. Montelione
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA; Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, UMDNJ, Piscataway NJ 08854, USA
| | - Michael A. Kennedy
- Department of Chemistry and Biochemistry, Miami University, and Northeast Structural Genomics Consortium, Oxford, OH 45056, USA
| | - Thomas Szyperski
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, NY 14260, USA
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107
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Uemura Y, Nakagawa N, Wakamatsu T, Kim K, Montelione GT, Hunt JF, Kuramitsu S, Masui R. Crystal structure of the ligand-binding form of nanoRNase from Bacteroides fragilis, a member of the DHH/DHHA1 phosphoesterase family of proteins. FEBS Lett 2013; 587:2669-74. [PMID: 23851074 PMCID: PMC4113422 DOI: 10.1016/j.febslet.2013.06.053] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [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: 03/11/2013] [Revised: 06/25/2013] [Accepted: 07/01/2013] [Indexed: 01/07/2023]
Abstract
NanoRNase (Nrn) specifically degrades nucleoside 3',5'-bisphosphate and the very short RNA, nanoRNA, during the final step of mRNA degradation. The crystal structure of Nrn in complex with a reaction product GMP was determined. The overall structure consists of two domains that are interconnected by a flexible loop and form a cleft. Two Mn²⁺ ions are coordinated by conserved residues in the DHH motif of the N-terminal domain. GMP binds near the DHHA1 motif region in the C-terminal domain. Our structure enables us to predict the substrate-bound form of Nrn as well as other DHH/DHHA1 phosphoesterase family proteins.
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Affiliation(s)
- Yuri Uemura
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Noriko Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan,RIKEN SPring-8 Center, Japan
| | - Taisuke Wakamatsu
- Microbial Genetic Division, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Kwang Kim
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Gaetano T. Montelione
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - John F. Hunt
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, United States
| | - Seiki Kuramitsu
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan,Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan,RIKEN SPring-8 Center, Japan
| | - Ryoji Masui
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan,RIKEN SPring-8 Center, Japan,Corresponding author: Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1, Machikaneyama-cho, Toyonaka, Osaka 56-0043, Japan. Telephone: +81-6-6850-5434. Fax: +81-6-6850-5442. (R. Masui)
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108
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Tejero R, Snyder D, Mao B, Aramini JM, Montelione GT. PDBStat: a universal restraint converter and restraint analysis software package for protein NMR. J Biomol NMR 2013; 56:337-51. [PMID: 23897031 PMCID: PMC3932191 DOI: 10.1007/s10858-013-9753-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 06/11/2013] [Indexed: 05/20/2023]
Abstract
The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data formats required by software carrying out similar tasks, continue to confound the efforts of novices and experts alike. These important issues need to be addressed robustly in order to standardize protein NMR structure determination and validation. PDBStat is a C/C++ computer program originally developed as a universal coordinate and protein NMR restraint converter. Its primary function is to provide a user-friendly tool for interconverting between protein coordinate and protein NMR restraint data formats. It also provides an integrated set of computational methods for protein NMR restraint analysis and structure quality assessment, relabeling of prochiral atoms with correct IUPAC names, as well as multiple methods for analysis of the consistency of atomic positions indicated by their convergence across a protein NMR ensemble. In this paper we provide a detailed description of the PDBStat software, and highlight some of its valuable computational capabilities. As an example, we demonstrate the use of the PDBStat restraint converter for restrained CS-Rosetta structure generation calculations, and compare the resulting protein NMR structure models with those generated from the same NMR restraint data using more traditional structure determination methods. These results demonstrate the value of a universal restraint converter in allowing the use of multiple structure generation methods with the same restraint data for consensus analysis of protein NMR structures and the underlying restraint data.
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Affiliation(s)
- Roberto Tejero
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey and Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, and Northeast Structural Genomics Consortium, 679 Hoes Lane, Piscataway, New Jersey, 08854, USA
- Departamento de Quίmica Fίsica, Universidad de Valencia, Avenida Dr. Moliner 50 46100 Burjassot, Valencia, SPAIN
| | - David Snyder
- Department of Chemistry, William Paterson University, 300 Pompton Road Wayne, New Jersey 07470, USA
| | - Binchen Mao
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey and Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, and Northeast Structural Genomics Consortium, 679 Hoes Lane, Piscataway, New Jersey, 08854, USA
| | - James M. Aramini
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey and Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, and Northeast Structural Genomics Consortium, 679 Hoes Lane, Piscataway, New Jersey, 08854, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey and Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, and Northeast Structural Genomics Consortium, 679 Hoes Lane, Piscataway, New Jersey, 08854, USA
- To whom correspondence should be addressed: Prof. Gaetano T. Montelione CABM, Rutgers University 679 Hoes Lane Piscataway, NJ 08854-5638 Phone: 732-235-5321
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109
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Procko E, Hedman R, Hamilton K, Seetharaman J, Fleishman SJ, Su M, Aramini J, Kornhaber G, Hunt JF, Tong L, Montelione GT, Baker D. Computational design of a protein-based enzyme inhibitor. J Mol Biol 2013; 425:3563-75. [PMID: 23827138 DOI: 10.1016/j.jmb.2013.06.035] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [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: 04/23/2013] [Revised: 06/15/2013] [Accepted: 06/25/2013] [Indexed: 01/30/2023]
Abstract
While there has been considerable progress in designing protein-protein interactions, the design of proteins that bind polar surfaces is an unmet challenge. We describe the computational design of a protein that binds the acidic active site of hen egg lysozyme and inhibits the enzyme. The design process starts with two polar amino acids that fit deep into the enzyme active site, identifies a protein scaffold that supports these residues and is complementary in shape to the lysozyme active-site region, and finally optimizes the surrounding contact surface for high-affinity binding. Following affinity maturation, a protein designed using this method bound lysozyme with low nanomolar affinity, and a combination of NMR studies, crystallography, and knockout mutagenesis confirmed the designed binding surface and orientation. Saturation mutagenesis with selection and deep sequencing demonstrated that specific designed interactions extending well beyond the centrally grafted polar residues are critical for high-affinity binding.
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Affiliation(s)
- Erik Procko
- Department of Biochemistry and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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110
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Froese DS, Forouhar F, Tran TH, Vollmar M, Kim YS, Lew S, Neely H, Seetharaman J, Shen Y, Xiao R, Acton TB, Everett JK, Cannone G, Puranik S, Savitsky P, Krojer T, Pilka ES, Kiyani W, Lee WH, Marsden BD, von Delft F, Allerston CK, Spagnolo L, Gileadi O, Montelione GT, Oppermann U, Yue WW, Tong L. Crystal structures of malonyl-coenzyme A decarboxylase provide insights into its catalytic mechanism and disease-causing mutations. Structure 2013; 21:1182-92. [PMID: 23791943 PMCID: PMC3701320 DOI: 10.1016/j.str.2013.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [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: 02/06/2013] [Revised: 05/09/2013] [Accepted: 05/09/2013] [Indexed: 01/17/2023]
Abstract
Malonyl-coenzyme A decarboxylase (MCD) is found from bacteria to humans, has important roles in regulating fatty acid metabolism and food intake, and is an attractive target for drug discovery. We report here four crystal structures of MCD from human, Rhodopseudomonas palustris, Agrobacterium vitis, and Cupriavidus metallidurans at up to 2.3 Å resolution. The MCD monomer contains an N-terminal helical domain involved in oligomerization and a C-terminal catalytic domain. The four structures exhibit substantial differences in the organization of the helical domains and, consequently, the oligomeric states and intersubunit interfaces. Unexpectedly, the MCD catalytic domain is structurally homologous to those of the GCN5-related N-acetyltransferase superfamily, especially the curacin A polyketide synthase catalytic module, with a conserved His-Ser/Thr dyad important for catalysis. Our structures, along with mutagenesis and kinetic studies, provide a molecular basis for understanding pathogenic mutations and catalysis, as well as a template for structure-based drug design. Structures of human and bacterial MCDs were determined at up to 2.3 Å resolution Distinct tetrameric and dimeric MCD oligomerizations were observed Unexpected homology to the GNAT superfamily gives insights into catalytic mechanism The structures provide the molecular basis for the disease-causing mutations in MCD
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Affiliation(s)
- D Sean Froese
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
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111
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Forouhar F, Arragain S, Atta M, Gambarelli S, Mouesca JM, Hussain M, Xiao R, Kieffer-Jaquinod S, Seetharaman J, Acton TB, Montelione GT, Mulliez E, Hunt JF, Fontecave M. Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases. Nat Chem Biol 2013; 9:333-8. [PMID: 23542644 DOI: 10.1038/nchembio.1229] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 03/05/2013] [Indexed: 11/09/2022]
Abstract
How living organisms create carbon-sulfur bonds during the biosynthesis of critical sulfur-containing compounds is still poorly understood. The methylthiotransferases MiaB and RimO catalyze sulfur insertion into tRNAs and ribosomal protein S12, respectively. Both belong to a subgroup of radical-S-adenosylmethionine (radical-SAM) enzymes that bear two [4Fe-4S] clusters. One cluster binds S-adenosylmethionine and generates an Ado• radical via a well-established mechanism. However, the precise role of the second cluster is unclear. For some sulfur-inserting radical-SAM enzymes, this cluster has been proposed to act as a sacrificial source of sulfur for the reaction. In this paper, we report parallel enzymological, spectroscopic and crystallographic investigations of RimO and MiaB, which provide what is to our knowledge the first evidence that these enzymes are true catalysts and support a new sulfation mechanism involving activation of an exogenous sulfur cosubstrate at an exchangeable coordination site on the second cluster, which remains intact during the reaction.
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Affiliation(s)
- Farhad Forouhar
- Northeast Structural Genomics Consortium, New York, New York, USA
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112
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Mills JL, Acton TB, Xiao R, Everett JK, Montelione GT, Szyperski T. Solution NMR structure of the helicase associated domain BVU_0683(627-691) from Bacteroides vulgatus provides first structural coverage for protein domain family PF03457 and indicates domain binding to DNA. J Struct Funct Genomics 2013; 14:19-24. [PMID: 23160728 PMCID: PMC3637686 DOI: 10.1007/s10969-012-9148-0] [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] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/29/2012] [Indexed: 06/01/2023]
Abstract
A high-quality NMR structure of the helicase associated (HA) domain comprising residues 627-691 of the 753-residue protein BVU_0683 from Bacteroides vulgatus exhibits an all α-helical fold. The structure presented here is the first representative for the large protein domain family PF03457 (currently 742 members) of HA domains. Comparison with structurally similar proteins supports the hypothesis that HA domains bind to DNA and that binding specificity varies greatly within the family of HA domains constituting PF03457.
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Affiliation(s)
- Jeffrey L. Mills
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, NY 14260, USA
| | - Thomas B. Acton
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Rong Xiao
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - John K. Everett
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Gaetano T. Montelione
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA, Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway, NJ 08854, USA
| | - Thomas Szyperski
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, NY 14260, USA
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113
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Kim DM, Zheng H, Huang YJ, Montelione GT, Hunt JF. ATPase active-site electrostatic interactions control the global conformation of the 100 kDa SecA translocase. J Am Chem Soc 2013; 135:2999-3010. [PMID: 23167435 PMCID: PMC4134686 DOI: 10.1021/ja306361q] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [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] [Indexed: 11/28/2022]
Abstract
SecA is an intensively studied mechanoenzyme that uses ATP hydrolysis to drive processive extrusion of secreted proteins through a protein-conducting channel in the cytoplasmic membrane of eubacteria. The ATPase motor of SecA is strongly homologous to that in DEAD-box RNA helicases. It remains unclear how local chemical events in its ATPase active site control the overall conformation of an ~100 kDa multidomain enzyme and drive protein transport. In this paper, we use biophysical methods to establish that a single electrostatic charge in the ATPase active site controls the global conformation of SecA. The enzyme undergoes an ATP-modulated endothermic conformational transition (ECT) believed to involve similar structural mechanics to the protein transport reaction. We have characterized the effects of an isosteric glutamate-to-glutamine mutation in the catalytic base, a mutation which mimics the immediate electrostatic consequences of ATP hydrolysis in the active site. Calorimetric studies demonstrate that this mutation facilitates the ECT in Escherichia coli SecA and triggers it completely in Bacillus subtilis SecA. Consistent with the substantial increase in entropy observed in the course of the ECT, hydrogen-deuterium exchange mass spectrometry demonstrates that it increases protein backbone dynamics in domain-domain interfaces at remote locations from the ATPase active site. The catalytic glutamate is one of ~250 charged amino acids in SecA, and yet neutralization of its side chain charge is sufficient to trigger a global order-disorder transition in this 100 kDa enzyme. The intricate network of structural interactions mediating this effect couples local electrostatic changes during ATP hydrolysis to global conformational and dynamic changes in SecA. This network forms the foundation of the allosteric mechanochemistry that efficiently harnesses the chemical energy stored in ATP to drive complex mechanical processes.
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Affiliation(s)
- Dorothy M. Kim
- Department of Biological Sciences and Northeast Structural Genomics Consortium, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA
- Departments of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, NY 10032, USA
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey. Piscataway, New Jersey 08854
| | - Yuanpeng J. Huang
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Gaetano T. Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey. Piscataway, New Jersey 08854
| | - John F. Hunt
- Department of Biological Sciences and Northeast Structural Genomics Consortium, 702A Fairchild Center, MC2434, Columbia University, New York, NY 10027, USA
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114
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Rossi P, Barbieri CM, Aramini JM, Bini E, Lee HW, Janjua H, Xiao R, Acton TB, Montelione GT. Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome. Nucleic Acids Res 2013; 41:2756-68. [PMID: 23303792 PMCID: PMC3575825 DOI: 10.1093/nar/gks1348] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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] [Indexed: 11/12/2022] Open
Abstract
Single-stranded DNA (ssDNA) binding proteins are important in basal metabolic pathways for gene transcription, recombination, DNA repair and replication in all domains of life. Their main cellular role is to stabilize melted duplex DNA and protect genomic DNA from degradation. We have uncovered the molecular function of protein domain family domain of unknown function DUF2128 (PF09901) as a novel ssDNA binding domain. This bacterial domain strongly associates into a dimer and presents a highly positively charged surface that is consistent with its function in non-specific ssDNA binding. Lactococcus lactis YdbC is a representative of DUF2128. The solution NMR structures of the 20 kDa apo-YdbC dimer and YdbC:dT19G1 complex were determined. The ssDNA-binding energetics to YdbC were characterized by isothermal titration calorimetry. YdbC shows comparable nanomolar affinities for pyrimidine and mixed oligonucleotides, and the affinity is sufficiently strong to disrupt duplex DNA. In addition, YdbC binds with lower affinity to ssRNA, making it a versatile nucleic acid-binding domain. The DUF2128 family is related to the eukaryotic nuclear protein positive cofactor 4 (PC4) family and to the PUR family both by fold similarity and molecular function.
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Affiliation(s)
- Paolo Rossi
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and the Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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115
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Eletsky A, Jeong MY, Kim H, Lee HW, Xiao R, Pagliarini DJ, Prestegard JH, Winge DR, Montelione GT, Szyperski T. Solution NMR structure of yeast succinate dehydrogenase flavinylation factor Sdh5 reveals a putative Sdh1 binding site. Biochemistry 2012; 51:8475-7. [PMID: 23062074 PMCID: PMC3667956 DOI: 10.1021/bi301171u] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [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] [Indexed: 01/15/2023]
Abstract
The yeast mitochondrial protein Sdh5 is required for the covalent attachment of flavin adenine dinucleotide (FAD) to protein Sdh1, a subunit of the heterotetrameric enzyme succinate dehydrogenase. The NMR structure of Sdh5 represents the first eukaryotic structure of Pfam family PF03937 and reveals a conserved surface region, which likely represents a putative Sdh1-Sdh5 interaction interface. Point mutations in this region result in the loss of covalent flavinylation of Sdh1. Moreover, chemical shift perturbation measurements showed that Sdh5 does not bind FAD in vitro, indicating that it is not a simple cofactor transporter in vivo.
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Affiliation(s)
- Alexander Eletsky
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
| | - Mi-Young Jeong
- University of Utah Health Sciences Center, Departments of Medicine and Biochemistry and Mitochondrial Proteome Partnership, Salt Lake City, Utah 84132, United States
| | - Hyung Kim
- University of Utah Health Sciences Center, Departments of Medicine and Biochemistry and Mitochondrial Proteome Partnership, Salt Lake City, Utah 84132, United States
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
| | - Rong Xiao
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway, New Jersey 08854, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
| | - David J. Pagliarini
- Department of Biochemistry and the Mitochondrial Protein Partnership, The University of Wisconsin – Madison, Madison, Wisconsin 53562, United States
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
| | - Dennis R. Winge
- University of Utah Health Sciences Center, Departments of Medicine and Biochemistry and Mitochondrial Proteome Partnership, Salt Lake City, Utah 84132, United States
| | - Gaetano T. Montelione
- Center of Advanced Biotechnology and Medicine and Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, Piscataway, New Jersey 08854, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
| | - Thomas Szyperski
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
- Northeast Structural Genomics Consortium Supporting Information Placeholder
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116
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Richter F, Blomberg R, Khare SD, Kiss G, Kuzin AP, Smith AJT, Gallaher J, Pianowski Z, Helgeson RC, Grjasnow A, Xiao R, Seetharaman J, Su M, Vorobiev S, Lew S, Forouhar F, Kornhaber GJ, Hunt JF, Montelione GT, Tong L, Houk KN, Hilvert D, Baker D. Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. J Am Chem Soc 2012; 134:16197-206. [PMID: 22871159 DOI: 10.1021/ja3037367] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleophilic catalysis is a general strategy for accelerating ester and amide hydrolysis. In natural active sites, nucleophilic elements such as catalytic dyads and triads are usually paired with oxyanion holes for substrate activation, but it is difficult to parse out the independent contributions of these elements or to understand how they emerged in the course of evolution. Here we explore the minimal requirements for esterase activity by computationally designing artificial catalysts using catalytic dyads and oxyanion holes. We found much higher success rates using designed oxyanion holes formed by backbone NH groups rather than by side chains or bridging water molecules and obtained four active designs in different scaffolds by combining this motif with a Cys-His dyad. Following active site optimization, the most active of the variants exhibited a catalytic efficiency (k(cat)/K(M)) of 400 M(-1) s(-1) for the cleavage of a p-nitrophenyl ester. Kinetic experiments indicate that the active site cysteines are rapidly acylated as programmed by design, but the subsequent slow hydrolysis of the acyl-enzyme intermediate limits overall catalytic efficiency. Moreover, the Cys-His dyads are not properly formed in crystal structures of the designed enzymes. These results highlight the challenges that computational design must overcome to achieve high levels of activity.
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Affiliation(s)
- Florian Richter
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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117
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Ramelot TA, Rossi P, Forouhar F, Lee HW, Yang Y, Ni S, Unser S, Lew S, Seetharaman J, Xiao R, Acton TB, Everett JK, Prestegard JH, Hunt JF, Montelione GT, Kennedy MA. Structure of a specialized acyl carrier protein essential for lipid A biosynthesis with very long-chain fatty acids in open and closed conformations. Biochemistry 2012; 51:7239-49. [PMID: 22876860 DOI: 10.1021/bi300546b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [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 solution nuclear magnetic resonance (NMR) structures and backbone (15)N dynamics of the specialized acyl carrier protein (ACP), RpAcpXL, from Rhodopseudomonas palustris, in both the apo form and holo form modified by covalent attachment of 4'-phosphopantetheine at S37, are virtually identical, monomeric, and correspond to the closed conformation. The structures have an extra α-helix compared to the archetypical ACP from Escherichia coli, which has four helices, resulting in a larger opening to the hydrophobic cavity. Chemical shift differences between apo- and holo-RpAcpXL indicated some differences in the hinge region between α2 and α3 and in the hydrophobic cavity environment, but corresponding changes in nuclear Overhauser effect cross-peak patterns were not detected. In contrast to the NMR structures, apo-RpAcpXL was observed in an open conformation in crystals that diffracted to 2.0 Å resolution, which resulted from movement of α3. On the basis of the crystal structure, the predicted biological assembly is a homodimer. Although the possible biological significance of dimerization is unknown, there is potential that the resulting large shared hydrophobic cavity could accommodate the very long-chain fatty acid (28-30 carbons) that this specialized ACP is known to synthesize and transfer to lipid A. These structures are the first representatives of the AcpXL family and the first to indicate that dimerization may be important for the function of these specialized ACPs.
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Affiliation(s)
- Theresa A Ramelot
- Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056, United States.
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118
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Feldmann EA, Seetharaman J, Ramelot TA, Lew S, Zhao L, Hamilton K, Ciccosanti C, Xiao R, Acton TB, Everett JK, Tong L, Montelione GT, Kennedy MA. Solution NMR and X-ray crystal structures of Pseudomonas syringae Pspto_3016 from protein domain family PF04237 (DUF419) adopt a "double wing" DNA binding motif. ACTA ACUST UNITED AC 2012; 13:155-62. [PMID: 22865330 DOI: 10.1007/s10969-012-9140-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 07/03/2012] [Indexed: 01/13/2023]
Abstract
The protein Pspto_3016 is a 117-residue member of the protein domain family PF04237 (DUF419), which is to date a functionally uncharacterized family of proteins. In this report, we describe the structure of Pspto_3016 from Pseudomonas syringae solved by both solution NMR and X-ray crystallography at 2.5 Å resolution. In both cases, the structure of Pspto_3016 adopts a "double wing" α/β sandwich fold similar to that of protein YjbR from Escherichia coli and to the C-terminal DNA binding domain of the MotA transcription factor (MotCF) from T4 bacteriophage, along with other uncharacterized proteins. Pspto_3016 was selected by the Protein Structure Initiative of the National Institutes of Health and the Northeast Structural Genomics Consortium (NESG ID PsR293).
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Affiliation(s)
- Erik A Feldmann
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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119
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Swapna GVT, Rossi P, Montelione AF, Benach J, Yu B, Abashidze M, Seetharaman J, Xiao R, Acton TB, Tong L, Montelione GT. Three structural representatives of the PF06855 protein domain family from Staphyloccocus aureus and Bacillus subtilis have SAM domain-like folds and different functions. ACTA ACUST UNITED AC 2012; 13:163-70. [PMID: 22843344 DOI: 10.1007/s10969-012-9134-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 02/02/2012] [Indexed: 10/28/2022]
Abstract
Protein domain family PF06855 (DUF1250) is a family of small domains of unknown function found only in bacteria, and mostly in the order Bacillales and Lactobacillales. Here we describe the solution NMR or X-ray crystal structures of three representatives of this domain family, MW0776 and MW1311 from Staphyloccocus aureus and yozE from Bacillus subtilis. All three proteins adopt a four-helix motif similar to sterile alpha motif (SAM) domains. Phylogenetic analysis classifies MW1311 and yozE as functionally equivalent proteins of the UPF0346 family of unknown function, but excludes MW0776, which likely has a different biological function. Our structural characterization of the three domains supports this separation of function. The structures of MW0776, MW1311, and yozE constitute the first structural representatives from this protein domain family.
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Affiliation(s)
- G V T Swapna
- Center for Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, 08854, USA
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120
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Vorobiev SM, Neely H, Yu B, Seetharaman J, Xiao R, Acton TB, Montelione GT, Hunt JF. Crystal structure of a catalytically active GG(D/E)EF diguanylate cyclase domain from Marinobacter aquaeolei with bound c-di-GMP product. ACTA ACUST UNITED AC 2012; 13:177-83. [PMID: 22843345 DOI: 10.1007/s10969-012-9136-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 02/02/2012] [Indexed: 01/06/2023]
Abstract
Recent studies of signal transduction in bacteria have revealed a unique second messenger, bis-(3'-5')-cyclic dimeric GMP (c-di-GMP), which regulates transitions between motile states and sessile states, such as biofilms. C-di-GMP is synthesized from two GTP molecules by diguanylate cyclases (DGC). The catalytic activity of DGCs depends on a conserved GG(D/E)EF domain, usually part of a larger multi-domain protein organization. The domains other than the GG(D/E)EF domain often control DGC activation. This paper presents the 1.83 Å crystal structure of an isolated catalytically competent GG(D/E)EF domain from the A1U3W3_MARAV protein from Marinobacter aquaeolei. Co-crystallization with GTP resulted in enzymatic synthesis of c-di-GMP. Comparison with previously solved DGC structures shows a similar orientation of c-di-GMP bound to an allosteric regulatory site mediating feedback inhibition of the enzyme. Biosynthesis of c-di-GMP in the crystallization reaction establishes that the enzymatic activity of this DGC domain does not require interaction with regulatory domains.
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Affiliation(s)
- Sergey M Vorobiev
- Department of Biological Sciences, The Northeast Structural Genomics Consortium Columbia University, New York, NY, 10032, USA
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121
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Aziz A, Hess JF, Budamagunta MS, Voss JC, Kuzin AP, Huang YJ, Xiao R, Montelione GT, FitzGerald PG, Hunt JF. The structure of vimentin linker 1 and rod 1B domains characterized by site-directed spin-labeling electron paramagnetic resonance (SDSL-EPR) and X-ray crystallography. J Biol Chem 2012; 287:28349-61. [PMID: 22740688 DOI: 10.1074/jbc.m111.334011] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Despite the passage of ∼30 years since the complete primary sequence of the intermediate filament (IF) protein vimentin was reported, the structure remains unknown for both an individual protomer and the assembled filament. In this report, we present data describing the structure of vimentin linker 1 (L1) and rod 1B. Electron paramagnetic resonance spectra collected from samples bearing site-directed spin labels demonstrate that L1 is not a flexible segment between coiled-coils (CCs) but instead forms a rigid, tightly packed structure. An x-ray crystal structure of a construct containing L1 and rod 1B shows that it forms a tetramer comprising two equivalent parallel CC dimers that interact with one another in the form of a symmetrical anti-parallel dimer. Remarkably, the parallel CC dimers are themselves asymmetrical, which enables them to tetramerize rather than undergoing higher order oligomerization. This functionally vital asymmetry in the CC structure, encoded in the primary sequence of rod 1B, provides a striking example of evolutionary exploitation of the structural plasticity of proteins. EPR and crystallographic data consistently suggest that a very short region within L1 represents a minor local distortion in what is likely to be a continuous CC from the end of rod 1A through the entirety of rod 1B. The concordance of this structural model with previously published cross-linking and spectral data supports the conclusion that the crystallographic oligomer represents a native biological structure.
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Affiliation(s)
- Atya Aziz
- Department of Cell Biology and Human Anatomy, University of California, Davis, California 95616, USA
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122
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Rosato A, Aramini JM, Arrowsmith C, Bagaria A, Baker D, Cavalli A, Doreleijers JF, Eletsky A, Giachetti A, Guerry P, Gutmanas A, Güntert P, He Y, Herrmann T, Huang YJ, Jaravine V, Jonker HRA, Kennedy MA, Lange OF, Liu G, Malliavin TE, Mani R, Mao B, Montelione GT, Nilges M, Rossi P, van der Schot G, Schwalbe H, Szyperski TA, Vendruscolo M, Vernon R, Vranken WF, Vries SD, Vuister GW, Wu B, Yang Y, Bonvin AMJJ. Blind testing of routine, fully automated determination of protein structures from NMR data. Structure 2012; 20:227-36. [PMID: 22325772 DOI: 10.1016/j.str.2012.01.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 12/19/2011] [Accepted: 01/03/2012] [Indexed: 11/16/2022]
Abstract
The protocols currently used for protein structure determination by nuclear magnetic resonance (NMR) depend on the determination of a large number of upper distance limits for proton-proton pairs. Typically, this task is performed manually by an experienced researcher rather than automatically by using a specific computer program. To assess whether it is indeed possible to generate in a fully automated manner NMR structures adequate for deposition in the Protein Data Bank, we gathered 10 experimental data sets with unassigned nuclear Overhauser effect spectroscopy (NOESY) peak lists for various proteins of unknown structure, computed structures for each of them using different, fully automatic programs, and compared the results to each other and to the manually solved reference structures that were not available at the time the data were provided. This constitutes a stringent "blind" assessment similar to the CASP and CAPRI initiatives. This study demonstrates the feasibility of routine, fully automated protein structure determination by NMR.
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Affiliation(s)
- Antonio Rosato
- Magnetic Resonance Center, University of Florence, 50019 Sesto Fiorentino, Italy.
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123
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Wu Y, Punta M, Xiao R, Acton TB, Sathyamoorthy B, Dey F, Fischer M, Skerra A, Rost B, Montelione GT, Szyperski T. NMR structure of lipoprotein YxeF from Bacillus subtilis reveals a calycin fold and distant homology with the lipocalin Blc from Escherichia coli. PLoS One 2012; 7:e37404. [PMID: 22693626 PMCID: PMC3367933 DOI: 10.1371/journal.pone.0037404] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [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: 02/13/2012] [Accepted: 04/19/2012] [Indexed: 11/18/2022] Open
Abstract
The soluble monomeric domain of lipoprotein YxeF from the Gram positive bacterium B. subtilis was selected by the Northeast Structural Genomics Consortium (NESG) as a target of a biomedical theme project focusing on the structure determination of the soluble domains of bacterial lipoproteins. The solution NMR structure of YxeF reveals a calycin fold and distant homology with the lipocalin Blc from the Gram-negative bacterium E.coli. In particular, the characteristic β-barrel, which is open to the solvent at one end, is extremely well conserved in YxeF with respect to Blc. The identification of YxeF as the first lipocalin homologue occurring in a Gram-positive bacterium suggests that lipocalins emerged before the evolutionary divergence of Gram positive and Gram negative bacteria. Since YxeF is devoid of the α-helix that packs in all lipocalins with known structure against the β-barrel to form a second hydrophobic core, we propose to introduce a new lipocalin sub-family named ‘slim lipocalins’, with YxeF and the other members of Pfam family PF11631 to which YxeF belongs constituting the first representatives. The results presented here exemplify the impact of structural genomics to enhance our understanding of biology and to generate new biological hypotheses.
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Affiliation(s)
- Yibing Wu
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, United States of America
- Northeast Structural Genomics Consortium
| | - Marco Punta
- Department of Computer Science and Institute for Advanced Study, Technical University of Munich, Munich, Germany
- Northeast Structural Genomics Consortium
| | - Rong Xiao
- Center of Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, New Jersey, United States of America
- Northeast Structural Genomics Consortium
| | - Thomas B. Acton
- Center of Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, New Jersey, United States of America
- Northeast Structural Genomics Consortium
| | - Bharathwaj Sathyamoorthy
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Fabian Dey
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
- Northeast Structural Genomics Consortium
| | - Markus Fischer
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
- Northeast Structural Genomics Consortium
| | - Arne Skerra
- Munich Center for Integrated Protein Science, CIPS-M, and Lehrstuhl für Biologische Chemie, Technische Universität München, Freising-Weihenstephan, Germany
| | - Burkhard Rost
- Department of Computer Science and Institute for Advanced Study, Technical University of Munich, Munich, Germany
- Northeast Structural Genomics Consortium
| | - Gaetano T. Montelione
- Center of Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Robert Wood Johnson Medical School, The State University of New Jersey, Piscataway, New Jersey, United States of America
- Northeast Structural Genomics Consortium
| | - Thomas Szyperski
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, United States of America
- Northeast Structural Genomics Consortium
- * E-mail:
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Aramini JM, Petrey D, Lee DY, Janjua H, Xiao R, Acton TB, Everett JK, Montelione GT. Solution NMR structure of Alr2454 from Nostoc sp. PCC 7120, the first structural representative of Pfam domain family PF11267. ACTA ACUST UNITED AC 2012; 13:171-6. [PMID: 22592539 DOI: 10.1007/s10969-012-9135-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 02/02/2012] [Indexed: 10/28/2022]
Abstract
Protein domain family PF11267 (DUF3067) is a family of proteins of unknown function found in both bacteria and eukaryotes. Here we present the solution NMR structure of the 102-residue Alr2454 protein from Nostoc sp. PCC 7120, which constitutes the first structural representative from this conserved protein domain family. The structure of Nostoc sp. Alr2454 adopts a novel protein fold.
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Affiliation(s)
- James M Aramini
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA.
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125
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Abstract
We describe the RPF web server, a quality assessment tool for protein NMR structures. The RPF server measures the ‘goodness-of-fit’ of the 3D structure with NMR chemical shift and unassigned NOESY data, and calculates a discrimination power (DP) score, which estimates the differences between the fits of the query structures and random coil structures to these experimental data. The DP-score is an accuracy predictor of the query structure. The RPF server also maps local structure quality measures onto the 3D structure using an online molecular viewer, and onto the NMR spectra, allowing refinement of the structure and/or NOESY peak list data. The RPF server is available at: http://nmr.cabm.rutgers.edu/rpf.
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Affiliation(s)
- Yuanpeng Janet Huang
- Center for Advanced Biotechnology and Medicine, Northeast Structural Genomic Consortium, Rutgers University, 679 Hoes Lane, Piscataway, NJ 08854, USA
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126
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Aramini JM, Hamilton K, Rossi P, Ertekin A, Lee HW, Lemak A, Wang H, Xiao R, Acton TB, Everett JK, Montelione GT. Solution NMR structure, backbone dynamics, and heme-binding properties of a novel cytochrome c maturation protein CcmE from Desulfovibrio vulgaris. Biochemistry 2012; 51:3705-7. [PMID: 22497251 DOI: 10.1021/bi300457b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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
Cytochrome c maturation protein E, CcmE, plays an integral role in the transfer of heme to apocytochrome c in many prokaryotes and some mitochondria. A novel subclass featuring a heme-binding cysteine has been identified in archaea and some bacteria. Here we describe the solution NMR structure, backbone dynamics, and heme binding properties of the soluble C-terminal domain of Desulfovibrio vulgaris CcmE, dvCcmE'. The structure adopts a conserved β-barrel OB fold followed by an unstructured C-terminal tail encompassing the CxxxY heme-binding motif. Heme binding analyses of wild-type and mutant dvCcmE' demonstrate the absolute requirement of residue C127 for noncovalent heme binding in vitro.
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Affiliation(s)
- James M Aramini
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.
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127
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Abstract
The Protein Structure Initiative (PSI) was established in 2000 by the National Institutes of General Medical Sciences with the long-term goal of providing 3D (three-dimensional) structural information for most proteins in nature. As advances in genomic sequencing, bioinformatics, homology modelling, and methods for rapid determination of 3D structures of proteins by X-ray crystallography and nuclear magnetic resonance (NMR) converged, it was proposed that our understanding of the biology of protein structure and evolution could be greatly enabled by ‘genomic-scale’ protein structure determination. Over the past 12 years, the PSI has evolved from a testing bed for new methods of sample and structure production to a core component of a wide range of biology programs.
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Affiliation(s)
- Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
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128
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Kobayashi H, Swapna GVT, Wu KP, Afinogenova Y, Conover K, Mao B, Montelione GT, Inouye M. Segmental isotope labeling of proteins for NMR structural study using a protein S tag for higher expression and solubility. J Biomol NMR 2012; 52:303-313. [PMID: 22389115 PMCID: PMC4117381 DOI: 10.1007/s10858-012-9610-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 01/11/2012] [Indexed: 05/31/2023]
Abstract
A common obstacle to NMR studies of proteins is sample preparation. In many cases, proteins targeted for NMR studies are poorly expressed and/or expressed in insoluble forms. Here, we describe a novel approach to overcome these problems. In the protein S tag-intein (PSTI) technology, two tandem 92-residue N-terminal domains of protein S (PrS(2)) from Myxococcus xanthus is fused at the N-terminal end of a protein to enhance its expression and solubility. Using intein technology, the isotope-labeled PrS(2)-tag is replaced with non-isotope labeled PrS(2)-tag, silencing the NMR signals from PrS(2)-tag in isotope-filtered (1)H-detected NMR experiments. This method was applied to the E. coli ribosome binding factor A (RbfA), which aggregates and precipitates in the absence of a solubilization tag unless the C-terminal 25-residue segment is deleted (RbfAΔ25). Using the PrS(2)-tag, full-length well-behaved RbfA samples could be successfully prepared for NMR studies. PrS(2) (non-labeled)-tagged RbfA (isotope-labeled) was produced with the use of the intein approach. The well-resolved TROSY-HSQC spectrum of full-length PrS(2)-tagged RbfA superimposes with the TROSY-HSQC spectrum of RbfAΔ25, indicating that PrS(2)-tag does not affect the structure of the protein to which it is fused. Using a smaller PrS-tag, consisting of a single N-terminal domain of protein S, triple resonance experiments were performed, and most of the backbone (1)H, (15)N and (13)C resonance assignments for full-length E. coli RbfA were determined. Analysis of these chemical shift data with the Chemical Shift Index and heteronuclear (1)H-(15)N NOE measurements reveal the dynamic nature of the C-terminal segment of the full-length RbfA protein, which could not be inferred using the truncated RbfAΔ25 construct. CS-Rosetta calculations also demonstrate that the core structure of full-length RbfA is similar to that of the RbfAΔ25 construct.
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Affiliation(s)
- Hiroshi Kobayashi
- Department of Biochemistry, Robert Wood Johnson Medical School, Center for Advanced Biotechnology and Medicine, 679 Hoes Lane, Piscataway, NJ 08854, USA
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129
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Snyder DA, Aramini JM, Yu B, Huang YJ, Xiao R, Cort JR, Shastry R, Ma LC, Liu J, Rost B, Acton TB, Kennedy MA, Montelione GT. Solution NMR structure of the ribosomal protein RP-L35Ae from Pyrococcus furiosus. Proteins 2012; 80:1901-6. [PMID: 22422653 DOI: 10.1002/prot.24071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 03/03/2012] [Indexed: 11/08/2022]
Abstract
The ribosome consists of small and large subunits each composed of dozens of proteins and RNA molecules. However, the functions of many of the individual protomers within the ribosome are still unknown. In this article, we describe the solution NMR structure of the ribosomal protein RP-L35Ae from the archaeon Pyrococcus furiosus. RP-L35Ae is buried within the large subunit of the ribosome and belongs to Pfam protein domain family PF01247, which is highly conserved in eukaryotes, present in a few archaeal genomes, but absent in bacteria. The protein adopts a six-stranded anti-parallel β-barrel analogous to the "tRNA binding motif" fold. The structure of the P. furiosus RP-L35Ae presented in this article constitutes the first structural representative from this protein domain family.
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Affiliation(s)
- David A Snyder
- Department of Chemistry, College of Science and Health, William Paterson University, Wayne, New Jersey 07470, USA
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130
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Ertekin A, Aramini JM, Rossi P, Leonard PG, Janjua H, Xiao R, Maglaqui M, Lee HW, Prestegard JH, Montelione GT. Human cyclin-dependent kinase 2-associated protein 1 (CDK2AP1) is dimeric in its disulfide-reduced state, with natively disordered N-terminal region. J Biol Chem 2012; 287:16541-9. [PMID: 22427660 DOI: 10.1074/jbc.m112.343863] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
CDK2AP1 (cyclin-dependent kinase 2-associated protein 1), corresponding to the gene doc-1 (deleted in oral cancer 1), is a tumor suppressor protein. The doc-1 gene is absent or down-regulated in hamster oral cancer cells and in many other cancer cell types. The ubiquitously expressed CDK2AP1 protein is the only known specific inhibitor of CDK2, making it an important component of cell cycle regulation during G(1)-to-S phase transition. Here, we report the solution structure of CDK2AP1 by combined methods of solution state NMR and amide hydrogen/deuterium exchange measurements with mass spectrometry. The homodimeric structure of CDK2AP1 includes an intrinsically disordered 60-residue N-terminal region and a four-helix bundle dimeric structure with reduced Cys-105 in the C-terminal region. The Cys-105 residues are, however, poised for disulfide bond formation. CDK2AP1 is phosphorylated at a conserved Ser-46 site in the N-terminal "intrinsically disordered" region by IκB kinase ε.
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Affiliation(s)
- Asli Ertekin
- Center for Advanced Biotechnology and Medicine and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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131
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Eletsky A, Acton TB, Xiao R, Everett JK, Montelione GT, Szyperski T. Solution NMR structures reveal a distinct architecture and provide first structures for protein domain family PF04536. J Struct Funct Genomics 2012; 13:9-14. [PMID: 22198206 PMCID: PMC3609422 DOI: 10.1007/s10969-011-9122-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 12/13/2011] [Indexed: 11/29/2022]
Abstract
The protein family (Pfam) PF04536 is a broadly conserved domain family of unknown function (DUF477), with more than 1,350 members in prokaryotic and eukaryotic proteins. High-quality NMR structures of the N-terminal domain comprising residues 41-180 of the 684-residue protein CG2496 from Corynebacterium glutamicum and the N-terminal domain comprising residues 35-182 of the 435-residue protein PG0361 from Porphyromonas gingivalis both exhibit an α/β fold comprised of a four-stranded β-sheet, three α-helices packed against one side of the sheet, and a fourth α-helix attached to the other side. In spite of low sequence similarity (18%) assessed by structure-based sequence alignment, the two structures are globally quite similar. However, moderate structural differences are observed for the relative orientation of two of the four helices. Comparison with known protein structures reveals that the α/β architecture of CG2496(41-180) and PG0361(35-182) has previously not been characterized. Moreover, calculation of surface charge potential and identification of surface clefts indicate that the two domains very likely have different functions.
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Affiliation(s)
- Alexander Eletsky
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, NY 14260, USA
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132
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Eletsky A, Petrey D, Cliff Zhang Q, Lee HW, Acton TB, Xiao R, Everett JK, Prestegard JH, Honig B, Montelione GT, Szyperski T. Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771. J Struct Funct Genomics 2012; 13:1-7. [PMID: 22223187 PMCID: PMC3654790 DOI: 10.1007/s10969-011-9121-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 12/13/2011] [Indexed: 11/29/2022]
Abstract
High-quality NMR structures of the homo-dimeric proteins Bvu3908 (69-residues in monomeric unit) from Bacteroides vulgatus and Bt2368 (74-residues) from Bacteroides thetaiotaomicron reveal the presence of winged helix-turn-helix (wHTH) motifs mediating tight complex formation. Such homo-dimer formation by winged HTH motifs is otherwise found only in two DNA-binding proteins with known structure: the C-terminal wHTH domain of transcriptional activator FadR from E. coli and protein TubR from B. thurigensis, which is involved in plasmid DNA segregation. However, the relative orientation of the wHTH motifs is different and residues involved in DNA-binding are not conserved in Bvu3908 and Bt2368. Hence, the proteins of the present study are not very likely to bind DNA, but are likely to exhibit a function that has thus far not been ascribed to homo-dimers formed by winged HTH motifs. The structures of Bvu3908 and Bt2368 are the first atomic resolution structures for PFAM family PF10771, a family of unknown function (DUF2582) currently containing 128 members.
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Affiliation(s)
- Alexander Eletsky
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, NY 14260, USA
| | - Donald Petrey
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
| | - Qiangfeng Cliff Zhang
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, University of Georgia, and Northeast Structural Genomics Consortium, Athens, GA 30602, USA
| | - Thomas B. Acton
- Department of Molecular Biology and Biochemistry, Center of Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Rong Xiao
- Department of Molecular Biology and Biochemistry, Center of Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - John K. Everett
- Department of Molecular Biology and Biochemistry, Center of Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, and Northeast Structural Genomics Consortium, Athens, GA 30602, USA
| | - Barry Honig
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
| | - Gaetano T. Montelione
- Department of Molecular Biology and Biochemistry, Center of Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Biochemistry, Robert Wood Johnson Medical School, UMDNJ, and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
| | - Thomas Szyperski
- Department of Chemistry, The State University of New York at Buffalo, and Northeast Structural Genomics Consortium, Buffalo, NY 14260, USA
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133
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M. Vorobiev S, Janet Huang Y, Seetharaman J, Xiao R, B. Acton T, T. Montelione G, Tong L. Human Retinoblastoma Binding Protein 9, a Serine Hydrolase Implicated in Pancreatic Cancers. Protein Pept Lett 2012; 19:194-7. [DOI: 10.2174/092986612799080356] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Revised: 06/21/2011] [Accepted: 06/22/2011] [Indexed: 11/22/2022]
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134
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Cho EJ, Xia S, Ma LC, Robertus J, Krug RM, Anslyn EV, Montelione GT, Ellington AD. Identification of influenza virus inhibitors targeting NS1A utilizing fluorescence polarization-based high-throughput assay. ACTA ACUST UNITED AC 2012; 17:448-59. [PMID: 22223052 DOI: 10.1177/1087057111431488] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This article describes the development of a simple and robust fluorescence polarization (FP)-based binding assay and adaptation to high-throughput identification of small molecules blocking dsRNA binding to NS1A protein (nonstructural protein 1 from type A influenza strains). This homogeneous assay employs fluorescein-labeled 16-mer dsRNA and full-length NS1A protein tagged with glutathione S-transferase to monitor the changes in FP and fluorescence intensity simultaneously. The assay was optimized for high-throughput screening in a 384-well format and achieved a z' score greater than 0.7. Its feasibility for high-throughput screening was demonstrated using the National Institutes of Health clinical collection. Six of 446 small molecules were identified as possible ligands in an initial screening. A series of validation tests confirmed epigallocatechine gallate (EGCG) to be active in the submicromolar range. A mechanism of EGCG inhibition involving interaction with the dsRNA-binding motif of NS1A, including Arg38, was proposed. This structural information is anticipated to provide a useful basis for the modeling of antiflu therapeutic reagents. Overall, the FP-based binding assay demonstrated its superior capability for simple, rapid, inexpensive, and robust identification of NS1A inhibitors and validation of their activity targeting NS1A.
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Affiliation(s)
- Eun Jeong Cho
- Texas Institute for Drug and Diagnostic Development, University of Texas at Austin, Austin, TX 78712, USA.
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135
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Bagaria A, Jaravine V, Huang YJ, Montelione GT, Güntert P. Protein structure validation by generalized linear model root-mean-square deviation prediction. Protein Sci 2012; 21:229-38. [PMID: 22113924 DOI: 10.1002/pro.2007] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [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: 10/19/2011] [Revised: 11/17/2011] [Accepted: 11/19/2011] [Indexed: 01/03/2023]
Abstract
Large-scale initiatives for obtaining spatial protein structures by experimental or computational means have accentuated the need for the critical assessment of protein structure determination and prediction methods. These include blind test projects such as the critical assessment of protein structure prediction (CASP) and the critical assessment of protein structure determination by nuclear magnetic resonance (CASD-NMR). An important aim is to establish structure validation criteria that can reliably assess the accuracy of a new protein structure. Various quality measures derived from the coordinates have been proposed. A universal structural quality assessment method should combine multiple individual scores in a meaningful way, which is challenging because of their different measurement units. Here, we present a method based on a generalized linear model (GLM) that combines diverse protein structure quality scores into a single quantity with intuitive meaning, namely the predicted coordinate root-mean-square deviation (RMSD) value between the present structure and the (unavailable) "true" structure (GLM-RMSD). For two sets of structural models from the CASD-NMR and CASP projects, this GLM-RMSD value was compared with the actual accuracy given by the RMSD value to the corresponding, experimentally determined reference structure from the Protein Data Bank (PDB). The correlation coefficients between actual (model vs. reference from PDB) and predicted (model vs. "true") heavy-atom RMSDs were 0.69 and 0.76, for the two datasets from CASD-NMR and CASP, respectively, which is considerably higher than those for the individual scores (-0.24 to 0.68). The GLM-RMSD can thus predict the accuracy of protein structures more reliably than individual coordinate-based quality scores.
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Affiliation(s)
- Anurag Bagaria
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, and Frankfurt Institute of Advanced Studies, Goethe University Frankfurt, Frankfurt am Main, Germany
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136
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Ramelot TA, Yang Y, Xiao R, Acton TB, Everett JK, Montelione GT, Kennedy MA. Solution NMR structure of BT_0084, a conjugative transposon lipoprotein from Bacteroides thetaiotamicron. Proteins 2011; 80:667-70. [PMID: 22116783 DOI: 10.1002/prot.23235] [Citation(s) in RCA: 2] [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: 07/23/2011] [Revised: 09/14/2011] [Accepted: 09/20/2011] [Indexed: 11/08/2022]
Abstract
Here we describe the solution NMR structure of the 120 amino acid fragment of BT_0084, without the N-terminal lipoprotein targeting sequence, encoded in a conjugative transposon (CTn) in the genome of Bacteroides thetaiotamicron. BT_0084 belongs to a conserved family of TraQ lipoproteins that are encoded at the end of the tra operon, which contains genes essential for transfer of CTns. The structure belongs to the immunoglobulin superfamily and shares structural similarity, albeit low sequence identity (< 15%), to other proteins involved in pili production for bacterial cell attachment. Although its role in repression of CTn transfer remains to be determined, the structure of BT_0084 reported here represents the first from the Bacteroides TraQ family and should facilitate further understanding of the tra operon-regulated transfer of CTns.
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Affiliation(s)
- Theresa A Ramelot
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056 and the Northeast Structural Genomics Consortium.
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137
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Feldmann EA, Ramelot TA, Yang Y, Xiao R, Acton TB, Everett JK, Montelione GT, Kennedy MA. Solution NMR structure of Asl3597 from Nostoc sp. PCC7120, the first structure from protein domain family PF12095, reveals a novel fold. Proteins 2011; 80:671-5. [PMID: 22113821 DOI: 10.1002/prot.23236] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 08/22/2011] [Accepted: 09/11/2011] [Indexed: 11/08/2022]
Abstract
The protein domain family PF12095 (DUF3571) is a functionally uncharacterized family of small proteins conserved from cyanobacteria to plants that are typically 85 to 95 amino acids in length in cyanobacteria. In this report, we describe the solution NMR structure of the 86-residue protein Asl3597 from Nostoc sp. PCC7120. The structure of Asl3597, which constitutes the first three-dimensional structure from protein family PF12095, has a unique α/β sandwich fold consisting of four anti-parallel β-strands opposite three continuous α-helices. Asl3597 may have a role in the assembly of the hydrophilic subcomplex of the cyanobacterial NAD(P)H complex as suggested by data for the orthologous Chlororespiratory reduction 7 protein from Arabidopsis thaliana.
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Affiliation(s)
- Erik A Feldmann
- Department of Chemistry and Biochemistry and the Northeast Structural Genomics Consortium, Miami University, Oxford, Ohio 45056
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138
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Forouhar F, Saadat N, Hussain M, Seetharaman J, Lee I, Janjua H, Xiao R, Shastry R, Acton TB, Montelione GT, Tong L. A large conformational change in the putative ATP pyrophosphatase PF0828 induced by ATP binding. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1323-1327. [PMID: 22102225 PMCID: PMC3212444 DOI: 10.1107/s1744309111031447] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [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: 06/03/2011] [Accepted: 08/03/2011] [Indexed: 05/31/2023]
Abstract
ATP pyrophosphatases (ATP PPases) are widely distributed in archaea and eukaryotes. They share an HUP domain at the N-terminus with a conserved PP-motif that interacts with the phosphates of ATP. The PF0828 protein from Pyrococcus furiosus is a member of the ATP PPase superfamily and it also has a 100-residue C-terminal extension that contains a strictly conserved EGG(E/D)xE(T/S) motif, which has been named the EGT-motif. Here, crystal structures of PF0828 alone and in complex with ATP or AMP are reported. The HUP domain contains a central five-stranded β-sheet that is surrounded by four helices, as in other related structures. The C-terminal extension forms a separate domain, named the EGT domain, which makes tight interactions with the HUP domain, bringing the EGT-motif near to the PP-motif and defining the putative active site of PF0828. Both motifs interact with the phosphate groups of ATP. A loop in the HUP domain undergoes a large conformational change to recognize the adenine base of ATP. In solution and in the crystal PF0828 is a dimer formed by the side-by-side arrangement of the HUP domains of the two monomers. The putative active site is located far from the dimer interface.
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Affiliation(s)
- Farhad Forouhar
- Northeast Structural Genomics Consortium, USA
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Nabila Saadat
- Northeast Structural Genomics Consortium, USA
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Munif Hussain
- Northeast Structural Genomics Consortium, USA
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Jayaraman Seetharaman
- Northeast Structural Genomics Consortium, USA
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Insun Lee
- Northeast Structural Genomics Consortium, USA
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Haleema Janjua
- Northeast Structural Genomics Consortium, USA
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
- Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Rong Xiao
- Northeast Structural Genomics Consortium, USA
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
- Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Ritu Shastry
- Northeast Structural Genomics Consortium, USA
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
- Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Thomas B. Acton
- Northeast Structural Genomics Consortium, USA
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
- Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Gaetano T. Montelione
- Northeast Structural Genomics Consortium, USA
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
- Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | - Liang Tong
- Northeast Structural Genomics Consortium, USA
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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139
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Kryshtafovych A, Moult J, Bartual SG, Bazan JF, Berman H, Casteel DE, Christodoulou E, Everett JK, Hausmann J, Heidebrecht T, Hills T, Hui R, Hunt JF, Seetharaman J, Joachimiak A, Kennedy MA, Kim C, Lingel A, Michalska K, Montelione GT, Otero JM, Perrakis A, Pizarro JC, van Raaij MJ, Ramelot TA, Rousseau F, Tong L, Wernimont AK, Young J, Schwede T. Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Proteins 2011; 79 Suppl 10:6-20. [PMID: 22020785 PMCID: PMC3692002 DOI: 10.1002/prot.23196] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [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] [Indexed: 11/07/2022]
Abstract
One goal of the CASP community wide experiment on the critical assessment of techniques for protein structure prediction is to identify the current state of the art in protein structure prediction and modeling. A fundamental principle of CASP is blind prediction on a set of relevant protein targets, that is, the participating computational methods are tested on a common set of experimental target proteins, for which the experimental structures are not known at the time of modeling. Therefore, the CASP experiment would not have been possible without broad support of the experimental protein structural biology community. In this article, several experimental groups discuss the structures of the proteins which they provided as prediction targets for CASP9, highlighting structural and functional peculiarities of these structures: the long tail fiber protein gp37 from bacteriophage T4, the cyclic GMP-dependent protein kinase Iβ dimerization/docking domain, the ectodomain of the JTB (jumping translocation breakpoint) transmembrane receptor, Autotaxin in complex with an inhibitor, the DNA-binding J-binding protein 1 domain essential for biosynthesis and maintenance of DNA base-J (β-D-glucosyl-hydroxymethyluracil) in Trypanosoma and Leishmania, an so far uncharacterized 73 residue domain from Ruminococcus gnavus with a fold typical for PDZ-like domains, a domain from the phycobilisome core-membrane linker phycobiliprotein ApcE from Synechocystis, the heat shock protein 90 activators PFC0360w and PFC0270w from Plasmodium falciparum, and 2-oxo-3-deoxygalactonate kinase from Klebsiella pneumoniae.
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Affiliation(s)
- Andriy Kryshtafovych
- Genome Center, University of California-Davis, 451 Health Sciences Drive, Davis, CA 95616, USA
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140
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Yin C, Aramini JM, Ma LC, Cort JR, Swapna GVT, Krug RM, Montelione GT. Backbone and Ile-δ1, Leu, Val methyl 1H, 13C and 15N NMR chemical shift assignments for human interferon-stimulated gene 15 protein. Biomol NMR Assign 2011; 5:215-219. [PMID: 21544738 PMCID: PMC3167004 DOI: 10.1007/s12104-011-9303-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Accepted: 04/14/2011] [Indexed: 05/30/2023]
Abstract
Human interferon-stimulated gene 15 protein (ISG15), also called ubiquitin cross-reactive protein (UCRP), is the first identified ubiquitin-like protein containing two ubiquitin-like domains fused in tandem. The active form of ISG15 is conjugated to target proteins via the C-terminal glycine residue through an isopeptide bond in a manner similar to ubiquitin. The biological role of ISG15 is strongly associated with the modulation of cell immune function, and there is mounting evidence suggesting that many viral pathogens evade the host innate immune response by interfering with ISG15 conjugation to both host and viral proteins in a variety of ways. Here we report nearly complete backbone (1)H(N), (15)N, (13)C', and (13)C(α), as well as side chain (13)C(β), methyl (Ile-δ1, Leu, Val), amide (Asn, Gln), and indole N-H (Trp) NMR resonance assignments for the 157-residue human ISG15 protein. These resonance assignments provide the basis for future structural and functional solution NMR studies of the biologically important human ISG15 protein.
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Affiliation(s)
- Cuifeng Yin
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - James M. Aramini
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Li-Chung Ma
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John R. Cort
- Biological Sciences Division, Pacific Northwest National Laboratory, Northeast Structural Genomics Consortium, Richland, WA 99352, USA
| | - G. V. T. Swapna
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Robert M. Krug
- Section of Molecular Genetics and Microbiology, Institute for Cellular and Molecular Biology, University of Texas, Austin, TX 78712, USA
| | - Gaetano T. Montelione
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, NJ 08854, USA
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141
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Mao B, Guan R, Montelione GT. Improved technologies now routinely provide protein NMR structures useful for molecular replacement. Structure 2011; 19:757-66. [PMID: 21645849 DOI: 10.1016/j.str.2011.04.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 04/07/2011] [Accepted: 04/25/2011] [Indexed: 10/18/2022]
Abstract
Molecular replacement (MR) is widely used for addressing the phase problem in X-ray crystallography. Historically, crystallographers have had limited success using NMR structures as MR search models. Here, we report a comprehensive investigation of the utility of protein NMR ensembles as MR search models, using data for 25 pairs of X-ray and NMR structures solved and refined using modern NMR methods. Starting from NMR ensembles prepared by an improved protocol, FindCore, correct MR solutions were obtained for 22 targets. Based on these solutions, automatic model rebuilding could be done successfully. Rosetta refinement of NMR structures provided MR solutions for another two proteins. We also demonstrate that such properly prepared NMR ensembles and X-ray crystal structures have similar performance when used as MR search models for homologous structures, particularly for targets with sequence identity >40%.
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Affiliation(s)
- Binchen Mao
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, and Robert Wood Johnson Medical School, UMDNJ, Piscataway, NJ 08854, USA
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142
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Yang Y, Ramelot TA, Cort JR, Wang H, Ciccosanti C, Jiang M, Janjua H, Acton TB, Xiao R, Everett JK, Montelione GT, Kennedy MA. Solution NMR structure of Dsy0195 homodimer from Desulfitobacterium hafniense: first structure representative of the YabP domain family of proteins involved in spore coat assembly. J Struct Funct Genomics 2011; 12:175-9. [PMID: 21904870 DOI: 10.1007/s10969-011-9117-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 08/26/2011] [Indexed: 11/24/2022]
Abstract
Protein domain family YabP (PF07873) is a family of small protein domains that are conserved in a wide range of bacteria and involved in spore coat assembly during the process of sporulation. The 62-residue fragment of Dsy0195 from Desulfitobacterium hafniense, which belongs to the YabP family, exists as a homodimer in solution under the conditions used for structure determination using NMR spectroscopy. The structure of the Dsy0195 homodimer contains two identical 62-residue monomeric subunits, each consisting of five anti-parallel beta strands (β1, 23-29; β2, 31-38; β3, 41-46; β4, 49-59; β5, 69-80). The tertiary structure of the Dsy0195 monomer adopts a cylindrical fold composed of two beta sheets. The two monomer subunits fold into a homodimer about a single C2 symmetry axis, with the interface composed of two anti-parallel beta strands, β1-β1' and β5b-β5b', where β5b refers to the C-terminal half of the bent β5 strand, without any domain swapping. Potential functional regions of the Dsy0195 structure were predicted based on conserved sequence analysis. The Dsy0195 structure reported here is the first representative structure from the YabP family.
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Affiliation(s)
- Yunhuang Yang
- Department of Chemistry and Biochemistry, Miami University, 701 East High Street, Oxford, OH 45056, USA
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143
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Aramini JM, Rossi P, Fischer M, Xiao R, Acton TB, Montelione GT. Solution NMR structure of VF0530 from Vibrio fischeri reveals a nucleic acid-binding function. Proteins 2011; 79:2988-91. [PMID: 21905121 DOI: 10.1002/prot.23121] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2011] [Revised: 06/10/2011] [Accepted: 06/15/2011] [Indexed: 11/11/2022]
Abstract
Protein domain family PF09905 (DUF2132) is a family of small domains of unknown function that are conserved in a wide range of bacteria. Here we describe the solution NMR structure of the 80-residue VF0530 protein from Vibrio fischeri, the first structural representative from this protein domain family. We demonstrate that the structure of VF0530 adopts a unique four-helix motif that shows some similarity to the C-terminal double-stranded DNA (dsDNA) binding domain of RecA, as well as other nucleic acid binding domains. Moreover, gel shift binding data indicate a potential dsDNA binding role for VF0530.
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Affiliation(s)
- James M Aramini
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA.
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144
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Lowery J, Szul T, Seetharaman J, Jian X, Su M, Forouhar F, Xiao R, Acton TB, Montelione GT, Lin H, Wright JW, Lee E, Holloway ZG, Randazzo PA, Tong L, Sztul E. Novel C-terminal motif within Sec7 domain of guanine nucleotide exchange factors regulates ADP-ribosylation factor (ARF) binding and activation. J Biol Chem 2011; 286:36898-906. [PMID: 21828055 DOI: 10.1074/jbc.m111.230631] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
ADP-ribosylation factors (ARFs) and their activating guanine nucleotide exchange factors (GEFs) play key roles in membrane traffic and signaling. All ARF GEFs share a ∼200-residue Sec7 domain (Sec7d) that alone catalyzes the GDP to GTP exchange that activates ARF. We determined the crystal structure of human BIG2 Sec7d. A C-terminal loop immediately following helix J (loop>J) was predicted to form contacts with helix H and the switch I region of the cognate ARF, suggesting that loop>J may participate in the catalytic reaction. Indeed, we identified multiple alanine substitutions within loop>J of the full length and/or Sec7d of two large brefeldin A-sensitive GEFs (GBF1 and BIG2) and one small brefeldin A-resistant GEF (ARNO) that abrogated binding of ARF and a single alanine substitution that allowed ARF binding but inhibited GDP to GTP exchange. Loop>J sequences are highly conserved, suggesting that loop>J plays a crucial role in the catalytic activity of all ARF GEFs. Using GEF mutants unable to bind ARF, we showed that GEFs associate with membranes independently of ARF and catalyze ARF activation in vivo only when membrane-associated. Our structural, cell biological, and biochemical findings identify loop>J as a key regulatory motif essential for ARF binding and GDP to GTP exchange by GEFs and provide evidence for the requirement of membrane association during GEF activity.
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Affiliation(s)
- Jason Lowery
- Department of Cell Biology, University of Alabama, Birmingham, Alabama 35294, USA
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145
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Eletsky A, Ruyechan WT, Xiao R, Acton TB, Montelione GT, Szyperski T. Solution NMR structure of MED25(391-543) comprising the activator-interacting domain (ACID) of human mediator subunit 25. ACTA ACUST UNITED AC 2011; 12:159-66. [PMID: 21785987 DOI: 10.1007/s10969-011-9115-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 07/11/2011] [Indexed: 10/18/2022]
Abstract
The solution NMR structure of protein MED25(391-543), comprising the activator interacting domain (ACID) of subunit 25 of the human mediator, is presented along with the measurement of polypeptide backbone heteronuclear 15N-{1H} NOEs to identify fast internal motional modes. This domain interacts with the acidic transactivation domains of Herpes simplex type 1 (HSV-1) protein VP16 and the Varicella-zoster virus (VZV) major transactivator protein IE62, which initiate transcription of viral genes. The structure is similar to the β-barrel domains of the human protein Ku and the SPOC domain of human protein SHARP, and provides a starting point to understand the structural biology of initiation of HSV-1 and VZV gene activation. Homology models built for the two ACID domains of the prostate tumor overexpressed (PTOV1) protein using the structure of MED25(391-543) as a template suggest that differential biological activities of the ACID domains in MED25 and PTOV1 arise from modulation of quite similar protein-protein interactions by variable residues grouped around highly conserved charged surface areas.
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Affiliation(s)
- Alexander Eletsky
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, NY 14260, USA
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146
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Zhang H, Constantine R, Vorobiev S, Chen Y, Seetharaman J, Huang YJ, Xiao R, Montelione GT, Gerstner CD, Davis MW, Inana G, Whitby FG, Jorgensen EM, Hill CP, Tong L, Baehr W. UNC119 is required for G protein trafficking in sensory neurons. Nat Neurosci 2011; 14:874-80. [PMID: 21642972 DOI: 10.1038/nn.2835] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Indexed: 12/20/2022]
Abstract
UNC119 is widely expressed among vertebrates and other phyla. We found that UNC119 recognized the acylated N terminus of the rod photoreceptor transducin α (Tα) subunit and Caenorhabditis elegans G proteins ODR-3 and GPA-13. The crystal structure of human UNC119 at 1.95-Å resolution revealed an immunoglobulin-like β-sandwich fold. Pulldowns and isothermal titration calorimetry revealed a tight interaction between UNC119 and acylated Gα peptides. The structure of co-crystals of UNC119 with an acylated Tα N-terminal peptide at 2.0 Å revealed that the lipid chain is buried deeply into UNC119's hydrophobic cavity. UNC119 bound Tα-GTP, inhibiting its GTPase activity, thereby providing a stable UNC119-Tα-GTP complex capable of diffusing from the inner segment back to the outer segment after light-induced translocation. UNC119 deletion in both mouse and C. elegans led to G protein mislocalization. Thus, UNC119 is a Gα subunit cofactor essential for G protein trafficking in sensory cilia.
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Affiliation(s)
- Houbin Zhang
- Department of Ophthalmology, University of Utah Health Science Center, Salt Lake City, Utah, USA
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147
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Aramini JM, Ma LC, Zhou L, Schauder CM, Hamilton K, Amer BR, Mack TR, Lee HW, Ciccosanti CT, Zhao L, Xiao R, Krug RM, Montelione GT. Dimer interface of the effector domain of non-structural protein 1 from influenza A virus: an interface with multiple functions. J Biol Chem 2011; 286:26050-60. [PMID: 21622573 DOI: 10.1074/jbc.m111.248765] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Non-structural protein 1 from influenza A virus, NS1A, is a key multifunctional virulence factor composed of two domains: an N-terminal double-stranded RNA (dsRNA)-binding domain and a C-terminal effector domain (ED). Isolated RNA-binding and effector domains of NS1A both exist as homodimers in solution. Despite recent crystal structures of isolated ED and full-length NS1A proteins from different influenza virus strains, controversy remains over the actual biologically relevant ED dimer interface. Here, we report the biophysical properties of the NS1A ED from H3N2 influenza A/Udorn/307/1972 (Ud) virus in solution. Several lines of evidence, including (15)N NMR relaxation, NMR chemical shift perturbations, static light scattering, and analytical sedimentation equilibrium, demonstrate that Ud NS1A ED forms a relatively weak dimer in solution (K(d) = 90 ± 2 μm), featuring a symmetric helix-helix dimer interface. Mutations within and near this interface completely abolish dimerization, whereas mutations consistent with other proposed ED dimer interfaces have no effect on dimer formation. In addition, the critical Trp-187 residue in this interface serves as a sensitive NMR spectroscopic marker for the concentration-dependent dimerization of NS1A ED in solution. Finally, dynamic light scattering and gel shift binding experiments demonstrate that the ED interface plays a role in both the oligomerization and the dsRNA binding properties of the full-length NS1A protein. In particular, mutation of the critical tryptophan in the ED interface substantially reduces the propensity of full-length NS1A from different strains to oligomerize and results in a reduction in dsRNA binding affinity for full-length NS1A.
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Affiliation(s)
- James M Aramini
- Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA.
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148
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Yang Y, Ramelot TA, Cort JR, Wang D, Ciccosanti C, Hamilton K, Nair R, Rost B, Acton TB, Xiao R, Everett JK, Montelione GT, Kennedy MA. Solution NMR structure of photosystem II reaction center protein Psb28 from Synechocystis sp. Strain PCC 6803. Proteins 2011; 79:340-4. [PMID: 21058299 DOI: 10.1002/prot.22876] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yunhuang Yang
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, USA
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149
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You L, Cho EJ, Leavitt J, Ma LC, Montelione GT, Anslyn EV, Krug RM, Ellington A, Robertus JD. Synthesis and evaluation of quinoxaline derivatives as potential influenza NS1A protein inhibitors. Bioorg Med Chem Lett 2011; 21:3007-11. [PMID: 21478016 PMCID: PMC3114437 DOI: 10.1016/j.bmcl.2011.03.042] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [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: 01/18/2011] [Revised: 03/10/2011] [Accepted: 03/11/2011] [Indexed: 01/22/2023]
Abstract
A library of quinoxaline derivatives were prepared to target non-structural protein 1 of influenza A (NS1A) as a means to develop anti-influenza drug leads. An in vitro fluorescence polarization assay demonstrated that these compounds disrupted the dsRNA-NS1A interaction to varying extents. Changes of substituent at positions 2, 3 and 6 on the quinoxaline ring led to variance in responses. The most active compounds (35 and 44) had IC(50) values in the range of low micromolar concentration without exhibiting significant dsRNA intercalation. Compound 44 was able to inhibit influenza A/Udorn/72 virus growth.
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Affiliation(s)
- Lei You
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Eun Jeong Cho
- The Institute for Drug and Diagnostic Development, University of Texas at Austin, Austin, TX, 78712, USA
| | - John Leavitt
- Department of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Li-Chung Ma
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Gaetano T. Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
- Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Eric V. Anslyn
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Robert M. Krug
- Department of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Andrew Ellington
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jon D. Robertus
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX, 78712, USA
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150
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Nie Y, Xiao R, Xu Y, Montelione GT. Novel anti-Prelog stereospecific carbonyl reductases from Candida parapsilosis for asymmetric reduction of prochiral ketones. Org Biomol Chem 2011; 9:4070-8. [PMID: 21505708 DOI: 10.1039/c0ob00938e] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The application of biocatalysis to the synthesis of chiral molecules is one of the greenest technologies for the replacement of chemical routes due to its environmentally benign reaction conditions and unparalleled chemo-, regio- and stereoselectivities. We have been interested in searching for carbonyl reductase enzymes and assessing their substrate specificity and stereoselectivity. We now report a gene cluster identified in Candida parapsilosis that consists of four open reading frames including three putative stereospecific carbonyl reductases (scr1, scr2, and scr3) and an alcohol dehydrogenase (cpadh). These newly identified three stereospecific carbonyl reductases (SCRs) showed high catalytic activities for producing (S)-1-phenyl-1,2-ethanediol from 2-hydroxyacetophenone with NADPH as the coenzyme. Together with CPADH, all four enzymes from this cluster are carbonyl reductases with novel anti-Prelog stereoselectivity. SCR1 and SCR3 exhibited distinct specificities to acetophenone derivatives and chloro-substituted 2-hydroxyacetophenones, and especially very high activities towards ethyl 4-chloro-3-oxobutyrate, a β-ketoester with important pharmaceutical potential. Our study also showed that genomic mining is a powerful tool for the discovery of new enzymes.
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Affiliation(s)
- Yao Nie
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854, USA
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