1
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Takayama Y, Nakasako M. Similarity score for screening phase-retrieved maps in X-ray diffraction imaging - characterization in reciprocal space. JOURNAL OF SYNCHROTRON RADIATION 2024; 31:95-112. [PMID: 38054944 PMCID: PMC10833420 DOI: 10.1107/s1600577523009827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023]
Abstract
X-ray diffraction imaging (XDI) is utilized for visualizing the structures of non-crystalline particles in material sciences and biology. In the structural analysis, phase-retrieval (PR) algorithms are applied to the diffraction amplitude data alone to reconstruct the electron density map of a specimen particle projected along the direction of the incident X-rays. However, PR calculations may not lead to good convergence because of a lack of diffraction patterns in small-angle regions and Poisson noise in X-ray detection. Therefore, the PR calculation is still a bottleneck for the efficient application of XDI in the structural analyses of non-crystalline particles. For screening maps from hundreds of trial PR calculations, we have been using a score and measuring the similarity between a pair of retrieved maps. Empirically, probable maps approximating the particle structures gave a score smaller than a threshold value, but the reasons for the effectiveness of the score are still unclear. In this study, the score is characterized in terms of the phase differences between the structure factors of the retrieved maps, the usefulness of the score in screening the maps retrieved from experimental diffraction patterns is demonstrated, and the effective resolution of similarity-score-selected maps is discussed.
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Affiliation(s)
- Yuki Takayama
- Graduate School of Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Sayo-gun, Hyogo 679-5148, Japan
- Synchrotron Radiation Research Center, Hyogo Science and Technology Association, 1-490-2 Kouto, Shingu, Tatsuno, Hyogo 679-5148, Japan
- International Center for Synchrotron Radiation Innovation Smart, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai 980-8577, Japan
| | - Masayoshi Nakasako
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Sayo-gun, Hyogo 679-5148, Japan
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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2
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Deshpande A, Schormann N, Piepenbrink MS, Martinez Sobrido L, Kobie JJ, Walter MR. Structure and epitope of a neutralizing monoclonal antibody that targets the stem helix of β coronaviruses. FEBS J 2023. [PMID: 37014961 DOI: 10.1111/febs.16777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/24/2023] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Monoclonal antibodies that retain neutralizing activity against multiple coronavirus (CoV) lineages and variants of concern (VoC) must be developed to protect against future pandemics. These broadly neutralizing MAbs (BNMAbs) may be used as therapeutics and/or to assist in the rational design of vaccines that induce BNMAbs. 1249A8 is a BNMAb that targets the stem helix (SH) region of CoV spike (S) protein and neutralizes Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) original strain, delta, and omicron VoC, Severe Acute Respiratory Syndrome CoV (SARS-CoV), and Middle East Respiratory Syndrome CoV (MERS-CoV). To understand its mechanism of action, the crystal structure of 1249A8 bound to a MERS-CoV SH peptide was determined at 2.1 Å resolution. BNMAb 1249A8 mimics the SARS-CoV-2 S loop residues 743-749, which interacts with the N-terminal end of the SH helix in the S post-fusion conformation. The conformation of 1249A8-bound SH is distinct from the SH conformation observed in the post-fusion SARS-CoV-2 S structure, suggesting 1249A8 disrupts the secondary structure and refolding events required for CoV post-fusion S to initiate membrane fusion and ultimately infection. This study provides novel insights into the neutralization mechanisms of SH-targeting CoV BNMAbs that may inform vaccine development and the design of optimal BNMAb therapeutics.
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Affiliation(s)
- Ashlesha Deshpande
- Department of Microbiology, University of Alabama at Birmingham, AL, USA
| | - Nobert Schormann
- Department of Biochemistry, University of Alabama at Birmingham, AL, USA
| | - Mike S Piepenbrink
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, AL, USA
| | - Luis Martinez Sobrido
- Disease Intervention & Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - James J Kobie
- Division of Infectious Diseases, Department of Medicine, University of Alabama at Birmingham, AL, USA
| | - Mark R Walter
- Department of Microbiology, University of Alabama at Birmingham, AL, USA
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3
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Huber EM, Kreling L, Heinrich AK, Dünnebacke M, Pöthig A, Bode HB, Groll M. A set of closely related methyltransferases for site-specific tailoring of anthraquinone pigments. Structure 2023; 31:573-583.e5. [PMID: 36963398 DOI: 10.1016/j.str.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/26/2023]
Abstract
Modification of the polyketide anthraquinone AQ-256 in the entomopathogenic Photorhabdus luminescens involves several O-methylations, but the biosynthetic gene cluster antA-I lacks corresponding tailoring enzymes. We here describe the identification of five putative, highly homologous O-methyltransferases encoded in the genome of P. luminescens. Activity assays in vitro and deletion experiments in vivo revealed that three of them account for anthraquinone tailoring by producing three monomethylated and two dimethylated species of AQ-256. X-ray structures of all five enzymes indicate high structural and mechanistic similarity. As confirmed by structure-based mutagenesis, a conserved histidine at the active site likely functions as a general base for substrate deprotonation and subsequent methyl transfer in all enzymes. Eight complex structures with AQ-256 as well as mono- and dimethylated derivatives confirm the substrate specificity patterns found in vitro and visualize how single amino acid differences in the active-site pockets impact substrate orientation and govern site-specific methylation.
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Affiliation(s)
- Eva M Huber
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany.
| | - Lukas Kreling
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Antje K Heinrich
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Maximilian Dünnebacke
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Alexander Pöthig
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Catalysis Research Center, Chair of Inorganic and Metal-Organic Chemistry, Ernst-Otto-Fischer-Str. 1, 85748 Garching, Germany
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany; Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; Chemical Biology, Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, 35043 Marburg, Germany; Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany.
| | - Michael Groll
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Protein Assemblies, Chair of Biochemistry, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany.
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4
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Mordhorst S, Badmann T, Bösch NM, Morinaka BI, Rauch H, Piel J, Groll M, Vagstad AL. Structural and Biochemical Insights into Post-Translational Arginine-to-Ornithine Peptide Modifications by an Atypical Arginase. ACS Chem Biol 2023; 18:528-536. [PMID: 36791048 PMCID: PMC10028609 DOI: 10.1021/acschembio.2c00879] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Landornamide A is a ribosomally synthesized and post-translationally modified peptide (RiPP) natural product with antiviral activity. Its biosynthetic gene cluster encodes─among other maturases─the peptide arginase OspR, which converts arginine to ornithine units in an unusual post-translational modification. Peptide arginases are a recently discovered RiPP maturase family with few characterized representatives. They show little sequence similarity to conventional arginases, a well-characterized enzyme family catalyzing the hydrolysis of free arginine to ornithine and urea. Peptide arginases are highly promiscuous and accept a variety of substrate sequences. The molecular basis for binding the large peptide substrate and for the high promiscuity of peptide arginases remains unclear. Here, we report the first crystal structure of a peptide arginase at a resolution of 2.6 Å. The three-dimensional structure reveals common features and differences between conventional arginases and the peptide arginase: the binuclear metal cluster and the active-site environment strongly resemble each other, while the quaternary structures diverge. Kinetic analyses of OspR with various substrates provide new insights into the order of biosynthetic reactions during the post-translational maturation of landornamide A. These results provide the basis for pathway engineering to generate derivatives of landornamide A and for the general application of peptide arginases as biosynthetic tools for peptide engineering.
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Affiliation(s)
- Silja Mordhorst
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Thomas Badmann
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Nina M Bösch
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Brandon I Morinaka
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Hartmut Rauch
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Anna L Vagstad
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
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5
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Fraley AE, Dell M, Schmalhofer M, Meoded RA, Bergande C, Groll M, Piel J. Heterocomplex structure of a polyketide synthase component involved in modular backbone halogenation. Structure 2023; 31:565-572.e4. [PMID: 36917986 DOI: 10.1016/j.str.2023.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/14/2022] [Accepted: 02/15/2023] [Indexed: 03/14/2023]
Abstract
Bacterial modular polyketide synthases (PKSs) generate diverse, complex and bioactive natural products that are constructed mainly based on principles of fatty acid biosynthesis. The cytotoxic oocydin-type polyketides contain a vinyl chloride moiety introduced during polyketide chain elongation. Required for modular polyketide backbone halogenation are a non-heme iron and ɑ-ketoglutarate-dependent halogenase OocP and OocQ lacking characterized homologs. This work provides structural insights into these unusual PKS components and their interactions via a high-resolution X-ray crystallography structure of the heterocomplex. By mapping the protein-protein interactions and comparison with structures of similar halogenases, we illustrate the potential of this heterodimer complex as a replacement for the conserved homodimeric structure of homologous enzymes. The OocPQ protein pair has thus evolved as a means of stabilizing the halogenase and facilitating chemical transformations with great synthetic utility.
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Affiliation(s)
- Amy E Fraley
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Maria Dell
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Maximilian Schmalhofer
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Strasse 8, 85748 Garching, Germany
| | - Roy A Meoded
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Cedric Bergande
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Strasse 8, 85748 Garching, Germany
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
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Structural and Biochemical Characterization of a Nonbinding SusD-Like Protein Involved in Xylooligosaccharide Utilization by an Uncultured Human Gut Bacteroides Strain. mSphere 2022; 7:e0024422. [PMID: 36043703 PMCID: PMC9599597 DOI: 10.1128/msphere.00244-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the human gut microbiota, Bacteroidetes break down dietary and endogenous glycosides through highly specific polysaccharide utilization loci (PULs). PULs encode a variety of sensor regulators, binding proteins, transporters, and carbohydrate-active enzymes (CAZymes). Surface glycan-binding proteins (SGBPs) are essential for the efficient capture of the glycosides present on the cell surface, providing Bacteroidetes with a competitive advantage in colonizing their habitats. Here, we present the functional and structural characterization of a SusD-like protein encoded by a xylooligosaccharide (XOS) PUL from an uncultured human gut Bacteroides strain. This locus is also conserved in Bacteroides vulgatus, thereby providing new mechanistic insights into the role of SGBPs in the metabolism of dietary fiber of importance for gut health. Various in vitro analyses, including saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy, revealed that the SusD-like protein cannot bind to the cognate substrate of the XOS PUL, although its presence is essential for the PUL to function. Analysis of the crystal structure of the SusD-like protein reveals an unfolded binding surface and the absence or inappropriate orientation of several key residues compared with other known SusD-like structures. These results highlight the critical role of the SusD-like protein in the transport of oligosaccharides and provide fundamental knowledge about the structure-function of SusC/D-like transporters, revealing that the binding specificity of SusD-like SGBPs does not necessarily reflect the uptake specificity of the transporter. IMPORTANCE The metabolization of dietary fiber is a crucial function for many gut bacteria, especially Bacteroidetes, which are particularly well adapted for recognizing, binding, transporting, and degrading glycosides. In this study, we report the functional and structural characterization of a SusD-like protein involved in xylooligosaccharide utilization by an uncultured gut Bacteroides strain. We demonstrate that while this protein is structurally similar to many canonical Bacteroidetes surface glycan-binding proteins, it cannot bind the substrate taken up by the cognate SusC-like transporter. This lack of binding might be explained by the absence of several key residues known to be involved in oligosaccharide binding and/or the possible necessity of the SusC-like protein to be present to create a cooperative binding site. The term “surface glycan-binding proteins” generally used for SusD-like proteins is thus not generic. Overall, this study allowed us to revisit the concept of glycoside utilization by Bacteroidetes, in particular those strains that feed on the short fibers naturally present in some dietary compounds or on the leftovers of other microbes.
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Baudrexl M, Fida T, Berk B, Schwarz WH, Zverlov VV, Groll M, Liebl W. Biochemical and Structural Characterization of Thermostable GH159 Glycoside Hydrolases Exhibiting α-L-Arabinofuranosidase Activity. Front Mol Biosci 2022; 9:907439. [PMID: 35847984 PMCID: PMC9278983 DOI: 10.3389/fmolb.2022.907439] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Functional, biochemical, and preliminary structural properties are reported for three glycoside hydrolases of the recently described glycoside hydrolase (GH) family 159. The genes were cloned from the genomic sequences of different Caldicellulosiruptor strains. This study extends the spectrum of functions of GH159 enzymes. The only activity previously reported for GH159 was hydrolytic activity on β-galactofuranosides. Activity screening using a set of para-nitrophenyl (pNP) glycosides suggested additional arabinosidase activity on substrates with arabinosyl residues, which has not been previously reported for members of GH159. Even though the thermophilic enzymes investigated—Cs_Gaf159A, Ch_Gaf159A, and Ck_Gaf159A—cleaved pNP-α-l-arabinofuranoside, they were only weakly active on arabinogalactan, and they did not cleave arabinose from arabinan, arabinoxylan, or gum arabic. However, the enzymes were able to hydrolyze the α-1,3-linkage in different arabinoxylan-derived oligosaccharides (AXOS) with arabinosylated xylose at the non-reducing end (A3X, A2,3XX), suggesting their role in the intracellular hydrolysis of oligosaccharides. Crystallization and structural analysis of the apo form of one of the Caldicellulosiruptor enzymes, Ch_Gaf159A, enabled the elucidation of the first 3D structure of a GH159 member. This work revealed a five-bladed β-propeller structure for GH159 enzymes. The 3D structure and its substrate-binding pocket also provides an explanation at the molecular level for the observed exo-activity of the enzyme. Furthermore, the structural data enabled the prediction of the catalytic amino acids. This was supported by the complete inactivation by mutation of residues D19, D142, and E190 of Ch_Gaf159A.
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Affiliation(s)
- Melanie Baudrexl
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Tarik Fida
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Berkay Berk
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | | | - Vladimir V. Zverlov
- Chair of Microbiology, Technical University of Munich, Freising, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Moscow, Russia
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Garching, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Freising, Germany
- *Correspondence: Wolfgang Liebl,
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8
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Esposito Verza A, Miggiano R, Lombardo F, Fiorillo C, Arcà B, Purghé B, Del Grosso E, Galli U, Rizzi M, Rossi F. Biochemical and structural analysis of a cytosolic sulfotransferase of the malaria vector Anopheles gambiae overexpressed in the reproductive tissues. Curr Res Struct Biol 2022; 4:246-255. [PMID: 35941867 PMCID: PMC9356239 DOI: 10.1016/j.crstbi.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/30/2022] [Accepted: 07/11/2022] [Indexed: 12/01/2022] Open
Abstract
The temporary or permanent chemical modification of biomolecules is a crucial aspect in the physiology of all living species. However, while some modules are well characterised also in insects, others did not receive the same attention. This holds true for sulfo-conjugation that is catalysed by cytosolic sulfotransferases (SULT), a central component of the metabolism of endogenous low molecular weight molecules and xenobiotics. In particular, limited information is available about the functional roles of the mosquito predicted enzymes annotated as SULTs in genomic databases. The herein described research is the first example of a biochemical and structural study of a SULT of a mosquito species, in general, and of the malaria vector Anopheles gambiae in particular. We confirmed that the AGAP001425 transcript displays a peculiar expression pattern that is suggestive of a possible involvement in modulating the mosquito reproductive tissues physiology, a fact that could raise attention on the enzyme as a potential target for insect-containment strategies. The crystal structures of the enzyme in alternative ligand-bound states revealed elements distinguishing AgSULT-001425 from other characterized SULTs, including a peculiar conformational plasticity of a discrete region that shields the catalytic cleft and that could play a main role in the dynamics of the reaction and in the substrate selectivity of the enzyme. Along with further in vitro biochemical studies, our structural investigations could provide a framework for the discovery of small-molecule inhibitors to assess the effect of interfering with AgSULT-001425-mediated catalysis at the organismal level. Mosquito cytosolic sulfotransferases (SULT) are poorly characterized. A SULT-encoding gene is highly transcribed in Anopheles male reproductive system. The corresponding enzyme is a genuine SULT acting on small phenolic molecules. We solved the AgSULT crystal structure in its substrate-free and ligand-bound states. The peculiar features of AgSULT could drive the design of isozyme-specific inhibitors.
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Affiliation(s)
- Arianna Esposito Verza
- University of Piemonte Orientale, DSF Department of Pharmaceutical Sciences, Largo Donegani, 2, Novara, Italy
| | - Riccardo Miggiano
- University of Piemonte Orientale, DSF Department of Pharmaceutical Sciences, Largo Donegani, 2, Novara, Italy
| | - Fabrizio Lombardo
- Sapienza University of Rome, Department of Public Health and Infectious Diseases – Division of Parasitology, Piazzale Aldo Moro, 5, Rome, Italy
| | - Carmine Fiorillo
- Sapienza University of Rome, Department of Public Health and Infectious Diseases – Division of Parasitology, Piazzale Aldo Moro, 5, Rome, Italy
| | - Bruno Arcà
- Sapienza University of Rome, Department of Public Health and Infectious Diseases – Division of Parasitology, Piazzale Aldo Moro, 5, Rome, Italy
| | - Beatrice Purghé
- University of Piemonte Orientale, DSF Department of Pharmaceutical Sciences, Largo Donegani, 2, Novara, Italy
| | - Erika Del Grosso
- University of Piemonte Orientale, DSF Department of Pharmaceutical Sciences, Largo Donegani, 2, Novara, Italy
| | - Ubaldina Galli
- University of Piemonte Orientale, DSF Department of Pharmaceutical Sciences, Largo Donegani, 2, Novara, Italy
| | - Menico Rizzi
- University of Piemonte Orientale, DSF Department of Pharmaceutical Sciences, Largo Donegani, 2, Novara, Italy
| | - Franca Rossi
- University of Piemonte Orientale, DSF Department of Pharmaceutical Sciences, Largo Donegani, 2, Novara, Italy
- Corresponding author. University of Piemonte Orientale DSF - Department of Pharmaceutical Sciences, Largo Donegani, 2 - 28100, Novara, Italy.
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Dong C, Liu Y, Lyu TJ, Beldar S, Lamb KN, Tempel W, Li Y, Li Z, James LI, Qin S, Wang Y, Min J. Structural Basis for the Binding Selectivity of Human CDY Chromodomains. Cell Chem Biol 2020; 27:827-838.e7. [DOI: 10.1016/j.chembiol.2020.05.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/21/2020] [Accepted: 05/11/2020] [Indexed: 01/22/2023]
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10
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Guo Y, Qiu W, Roche TE, Hackert ML. Crystal structure of the catalytic subunit of bovine pyruvate dehydrogenase phosphatase. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2020; 76:292-301. [PMID: 32627744 DOI: 10.1107/s2053230x20007943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/11/2020] [Indexed: 11/11/2022]
Abstract
Mammalian pyruvate dehydrogenase (PDH) activity is tightly regulated by phosphorylation and dephosphorylation, which is catalyzed by PDH kinase isomers and PDH phosphatase isomers, respectively. PDH phosphatase isomer 1 (PDP1) is a heterodimer consisting of a catalytic subunit (PDP1c) and a regulatory subunit (PDP1r). Here, the crystal structure of bovine PDP1c determined at 2.1 Å resolution is reported. The crystals belonged to space group P3221, with unit-cell parameters a = b = 75.3, c = 173.2 Å. The structure was solved by molecular-replacement methods and refined to a final R factor of 21.9% (Rfree = 24.7%). The final model consists of 402 of a possible 467 amino-acid residues of the PDP1c monomer, two Mn2+ ions in the active site, an additional Mn2+ ion coordinated by His410 and His414, two MnSO4 ion pairs at special positions near the crystallographic twofold symmetry axis and 226 water molecules. Several new features of the PDP1c structure are revealed. The requirements are described and plausible bases are deduced for the interaction of PDP1c with PDP1r and other components of the pyruvate dehydrogenase complex.
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Affiliation(s)
- Youzhong Guo
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Weihua Qiu
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Thomas E Roche
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS 66506, USA
| | - Marvin L Hackert
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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11
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Hortschansky P, Misslinger M, Mörl J, Gsaller F, Bromley MJ, Brakhage AA, Groll M, Haas H, Huber EM. Structural basis of HapE P88L-linked antifungal triazole resistance in Aspergillus fumigatus. Life Sci Alliance 2020; 3:3/7/e202000729. [PMID: 32467317 PMCID: PMC7266990 DOI: 10.26508/lsa.202000729] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/08/2020] [Accepted: 05/12/2020] [Indexed: 01/27/2023] Open
Abstract
Azoles are first-line therapeutics for human and plant fungal infections, but their broad use has promoted the development of resistances. Recently, a pan-azole-resistant clinical Aspergillus fumigatus isolate was identified to carry the mutation P88L in subunit HapE of the CCAAT-binding complex (CBC), a conserved eukaryotic transcription factor. Here, we define the mechanistic basis for resistance in this isolate by showing that the HapEP88L mutation interferes with the CBC's ability to bend and sense CCAAT motifs. This failure leads to transcriptional derepression of the cyp51A gene, which encodes the target of azoles, the 14-α sterol demethylase Cyp51A, and ultimately causes drug resistance. In addition, we demonstrate that the CBC-associated transcriptional regulator HapX assists cyp51A repression in low-iron environments and that this iron-dependent effect is lost in the HapEP88L mutant. Altogether, these results indicate that the mutation HapEP88L confers increased resistance to azoles compared with wt A. fumigatus, particularly in low-iron clinical niches such as the lung.
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Affiliation(s)
- Peter Hortschansky
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), and Friedrich Schiller University Jena, Jena, Germany
| | - Matthias Misslinger
- Institute of Molecular Biology/Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Jasmin Mörl
- Institute of Molecular Biology/Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Fabio Gsaller
- Institute of Molecular Biology/Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Michael J Bromley
- Manchester Fungal Infection Group, Institute of Inflammation and Repair, University of Manchester, Manchester, UK
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), and Friedrich Schiller University Jena, Jena, Germany
| | - Michael Groll
- Center for Integrated Protein Science Munich at the Department Chemistry, Technical University of Munich, Garching, Germany
| | - Hubertus Haas
- Institute of Molecular Biology/Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Eva M Huber
- Center for Integrated Protein Science Munich at the Department Chemistry, Technical University of Munich, Garching, Germany
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12
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Kazman P, Vielberg MT, Pulido Cendales MD, Hunziger L, Weber B, Hegenbart U, Zacharias M, Köhler R, Schönland S, Groll M, Buchner J. Fatal amyloid formation in a patient's antibody light chain is caused by a single point mutation. eLife 2020; 9:52300. [PMID: 32151314 PMCID: PMC7064341 DOI: 10.7554/elife.52300] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 02/06/2020] [Indexed: 11/29/2022] Open
Abstract
In systemic light chain amyloidosis, an overexpressed antibody light chain (LC) forms fibrils which deposit in organs and cause their failure. While it is well-established that mutations in the LC’s VL domain are important prerequisites, the mechanisms which render a patient LC amyloidogenic are ill-defined. In this study, we performed an in-depth analysis of the factors and mutations responsible for the pathogenic transformation of a patient-derived λ LC, by recombinantly expressing variants in E. coli. We show that proteolytic cleavage of the patient LC resulting in an isolated VL domain is essential for fibril formation. Out of 11 mutations in the patient VL, only one, a leucine to valine mutation, is responsible for fibril formation. It disrupts a hydrophobic network rendering the C-terminal segment of VL more dynamic and decreasing domain stability. Thus, the combination of proteolytic cleavage and the destabilizing mutation trigger conformational changes that turn the LC pathogenic. Amyloid light chain amyloidosis, shortened to AL amyloidosis, is a rare and often fatal disease. It is caused by a disorder of the bone marrow. Usually, cells in the bone marrow produce Y-shaped proteins called antibodies to fight infections. In AL amyloidosis, these cells release too much of the short arm of the antibody, known as its light chain, and the light chains also carry mutations. The antibodies are no longer able to assemble properly, and instead misfold and form structures, known as amyloid fibrils. The fibrils build up outside the cells, gradually causing damage to tissues and organs that can lead to life-threatening organ failure. Due to the rareness of the disease, diagnosis is often overlooked and delayed. People experience widely varying symptoms, depending on the organs affected. Also, given the diversity of antibodies people make, every person with AL amyloidosis has a variety of mutations implicated in their disease. It is thought that mutations in the antibody light chain make it unstable and prone to misfolding, but it remains unclear which specific mutations trigger a cascade of amyloid fibril formation. Now, Kazman et al. have pinpointed the exact mechanism in one case of the disease. First, tissue biopsies from a woman with advanced AL amyloidosis were analyzed, and the defunct antibody light chain was isolated. Eleven mutations were identified in the antibody light chain, only one of which was found to be responsible for the formation of the harmful fibrils. The next step was to determine how this one small change was so damaging. The experiments showed that after the antibody light chain was cut in two, a process that happens naturally in the body, this single mutation transforms it into a protein capable of causing disease. In this ‘bedside to lab bench’ study, Kazman et al. have succeeded in determining the molecular origin of one case of AL amyloidosis. The results have also shown that the instability of antibodies due to mutation does not alone explain the formation of amyloid fibrils in this disease and that the cutting of this protein in two is also important. It is hoped that, in the long run, this work will lead to new diagnostics and treatment options for people with AL amyloidosis.
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Affiliation(s)
- Pamina Kazman
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Marie-Theres Vielberg
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - María Daniela Pulido Cendales
- Center for Integrated Protein Science Munich at the Department Physik, Technische Universität München, Garching, Germany
| | - Lioba Hunziger
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Benedikt Weber
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Ute Hegenbart
- Medical Department V, Amyloidosis Center, University of Heidelberg, Heidelberg, Germany
| | - Martin Zacharias
- Center for Integrated Protein Science Munich at the Department Physik, Technische Universität München, Garching, Germany
| | - Rolf Köhler
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Stefan Schönland
- Medical Department V, Amyloidosis Center, University of Heidelberg, Heidelberg, Germany
| | - Michael Groll
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
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13
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Plasticity at the DNA recognition site of the MeCP2 mCG-binding domain. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194409. [PMID: 31356990 DOI: 10.1016/j.bbagrm.2019.194409] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/04/2019] [Accepted: 07/20/2019] [Indexed: 01/06/2023]
Abstract
MeCP2 is an abundant protein, involved in transcriptional repression by binding to CG and non-CG methylated DNA. However, MeCP2 might also function as a transcription activator as MeCP2 is found bound to sparsely methylated promoters of actively expressed genes. Furthermore, Attachment Region Binding Protein (ARBP), the chicken ortholog of MeCP2, has been reported to bind to Matrix/scaffold attachment regions (MARs/SARs) DNA with an unmethylated 5'-CAC/GTG-3' consensus sequence. In our previous study, although we have systemically measured the binding abilities of MBDs to unmethylated CAC/GTG DNA and the complex structures reveal that the MBD2-MBD (MBD of MBD2) binds to the unmethylated CAC/GTG DNA by recognizing the complementary GTG trinucleotide, how the MeCP2-MBD (MBD of MeCP2) recognizes the unmethylated CAC/GTG DNA, especially the MARs DNA, is still unclear. In this study, we investigated the binding characteristics of MeCP2 in recognizing unmethylated 5'-CAC/GTG-3' motif containing DNA by binding and structural studies. We found that MeCP2-MBD binds to MARs DNA with a comparable binding affinity to mCG DNA, and the MeCP2-CAC/GTG complex structure revealed that MeCP2 residues R111 and R133 form base-specific interactions with the GTG motif. For comparison, we also determined crystal structures of the MeCP2-MBD bound to mCG and mCAC/GTG DNA, respectively. Together, these crystal structures illustrate the adaptability of the MeCP2-MBD toward the GTG motif as well as the mCG DNA, and also provide structural basis of a biological role of MeCP2 as a transcription activator and its disease implications in Rett syndrome.
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14
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Chen S, Wiewiora RP, Meng F, Babault N, Ma A, Yu W, Qian K, Hu H, Zou H, Wang J, Fan S, Blum G, Pittella-Silva F, Beauchamp KA, Tempel W, Jiang H, Chen K, Skene RJ, Zheng YG, Brown PJ, Jin J, Luo C, Chodera JD, Luo M. The dynamic conformational landscape of the protein methyltransferase SETD8. eLife 2019; 8:45403. [PMID: 31081496 PMCID: PMC6579520 DOI: 10.7554/elife.45403] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/08/2019] [Indexed: 12/27/2022] Open
Abstract
Elucidating the conformational heterogeneity of proteins is essential for understanding protein function and developing exogenous ligands. With the rapid development of experimental and computational methods, it is of great interest to integrate these approaches to illuminate the conformational landscapes of target proteins. SETD8 is a protein lysine methyltransferase (PKMT), which functions in vivo via the methylation of histone and nonhistone targets. Utilizing covalent inhibitors and depleting native ligands to trap hidden conformational states, we obtained diverse X-ray structures of SETD8. These structures were used to seed distributed atomistic molecular dynamics simulations that generated a total of six milliseconds of trajectory data. Markov state models, built via an automated machine learning approach and corroborated experimentally, reveal how slow conformational motions and conformational states are relevant to catalysis. These findings provide molecular insight on enzymatic catalysis and allosteric mechanisms of a PKMT via its detailed conformational landscape. Our cells contain thousands of proteins that perform many different tasks. Such tasks often involve significant changes in the shape of a protein that allow it to interact with other proteins or ligands. Understanding these shape changes can be an essential step for predicting and manipulating how proteins work or designing new drugs. Some changes in protein shape happen quickly, whereas others take longer. Existing experimental approaches generally only capture some, but not all, of the different shapes an individual protein adopts. A family of proteins known as protein lysine methyltransferases (PKMTs) help to regulate the activities of other proteins by adding small tags called methyl groups to specific positions on their target proteins. PKMTs play important roles in many life processes including in activating genes, maintaining stem cells and controlling how organs develop. It is important for cells to properly control the activity of PKMTs because too much, or too little, activity can promote cancers and neurological diseases. For example, genetic mutations that increase the levels of a PKMT known as SETD8 appear to promote the progression of some breast cancers and childhood leukemia. There is a pressing need to develop new drugs that can inhibit SETD8 and other PKMTs in human patients. However, these efforts are hindered by the lack of understanding of exactly how the shape of PKMT proteins change as they operate in cells. Chen, Wiewiora et al. used a technique called X-ray crystallography to generate structural models of the human SETD8 protein in the presence or absence of native or foreign ligands. These models were used to develop computer simulations of how the shape of SETD8 changes as it operates. Further computational analysis and laboratory experiments revealed how slow changes in the shape of SETD8 contribute to the ability of the protein to attach methyl groups to other proteins. This work is a significant stepping-stone to developing a complete model of how the SETD8 protein works, as well as understanding how genetic mutations may affect the protein’s role in the body. The next step is to refine the model by integrating data from other approaches including biophysical models and mathematical calculations of the energy associated with the shape changes, with a long-term goal to better understand and then manipulate the function of SETD8.
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Affiliation(s)
- Shi Chen
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, United States.,Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Rafal P Wiewiora
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, United States.,Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Fanwang Meng
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Nicolas Babault
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Anqi Ma
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Wenyu Yu
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Kun Qian
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, United States
| | - Hao Hu
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, United States
| | - Hua Zou
- Takeda California, Science Center Drive, San Diego, United States
| | - Junyi Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Shijie Fan
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Gil Blum
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Fabio Pittella-Silva
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kyle A Beauchamp
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Hualiang Jiang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Kaixian Chen
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Robert J Skene
- Takeda California, Science Center Drive, San Diego, United States
| | - Yujun George Zheng
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, United States
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, United States.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Cheng Luo
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - John D Chodera
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Program of Pharmacology, Weill Cornell Medical College of Cornell University, New York, United States
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15
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Zhang J, Guo Q, Gao J, Xu C, Zhang B, Li M, She J, Shi Y, Zhang Z, Ruan K, Wu J. Structural insight into the unique dsDNA binding topology of the human ORC2 wing helix domain. FEBS J 2019; 286:2726-2736. [PMID: 30963726 DOI: 10.1111/febs.14844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 03/01/2019] [Accepted: 04/05/2019] [Indexed: 11/29/2022]
Abstract
The origin recognition complex (ORC) is indispensable for the initiation of DNA replication during the cell cycle. The DNA-binding modes of the human ORC winged helix domain (WHD) remain enigmatic, as the dsDNA recognition sites of archaeal and Saccharomyces cerevisiae ORC WHDs are distinct. Here, we solved the high-resolution crystal structure of the human ORC2 WHD, although its complex with dsDNA is difficult to crystallize due to its weak binding affinities. The near-complete NMR backbone assignments and chemical shift perturbations reveal a new dsDNA binding topology in addition to the conserved β-sheet hairpin region, in which residues show higher dynamics. The key interacting residues (R540, K548, and K549) were validated by mutagenesis studies. Our data suggest that the ORC2 WHD recognizes dsDNA sequences through its flexible β-sheet hairpin as an anchor point, while the rest of the protein adopts various orientations in different species. This weak but real interaction module identified by NMR is useful for the structural reconstruction of large biomolecular complexes using cryo-EM. The binding topology and dynamics of ORC2 WHDs were also underpinned by molecular dynamics simulations.
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Affiliation(s)
- Jiahai Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Qiong Guo
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Jun Gao
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Chao Xu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Beibei Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Mingwei Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Jiaqi She
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zhiyong Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ke Ruan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
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16
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Schopf FH, Huber EM, Dodt C, Lopez A, Biebl MM, Rutz DA, Mühlhofer M, Richter G, Madl T, Sattler M, Groll M, Buchner J. The Co-chaperone Cns1 and the Recruiter Protein Hgh1 Link Hsp90 to Translation Elongation via Chaperoning Elongation Factor 2. Mol Cell 2019; 74:73-87.e8. [PMID: 30876805 DOI: 10.1016/j.molcel.2019.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/17/2018] [Accepted: 02/07/2019] [Indexed: 12/31/2022]
Abstract
The Hsp90 chaperone machinery in eukaryotes comprises a number of distinct accessory factors. Cns1 is one of the few essential co-chaperones in yeast, but its structure and function remained unknown. Here, we report the X-ray structure of the Cns1 fold and NMR studies on the partly disordered, essential segment of the protein. We demonstrate that Cns1 is important for maintaining translation elongation, specifically chaperoning the elongation factor eEF2. In this context, Cns1 interacts with the novel co-factor Hgh1 and forms a quaternary complex together with eEF2 and Hsp90. The in vivo folding and solubility of eEF2 depend on the presence of these proteins. Chaperoning of eEF2 by Cns1 is essential for yeast viability and requires a defined subset of the Hsp90 machinery as well as the identified eEF2 recruiting factor Hgh1.
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Affiliation(s)
- Florian H Schopf
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Eva M Huber
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Christopher Dodt
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Abraham Lopez
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Maximilian M Biebl
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Daniel A Rutz
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Moritz Mühlhofer
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Gesa Richter
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany; Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria
| | - Tobias Madl
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany; Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria
| | - Michael Sattler
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Michael Groll
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science at the Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany.
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17
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Lukac I, Abdelhakim H, Ward RA, St-Gallay SA, Madden JC, Leach AG. Predicting protein-ligand binding affinity and correcting crystal structures with quantum mechanical calculations: lactate dehydrogenase A. Chem Sci 2019; 10:2218-2227. [PMID: 30881647 PMCID: PMC6388092 DOI: 10.1039/c8sc04564j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/19/2018] [Indexed: 12/22/2022] Open
Abstract
Accurately computing the geometry and energy of host-guest and protein-ligand interactions requires a physically accurate description of the forces in action. Quantum mechanics can provide this accuracy but the calculations can require a prohibitive quantity of computational resources. The size of the calculations can be reduced by including only the atoms of the receptor that are in close proximity to the ligand. We show that when combined with log P values for the ligand (which can be computed easily) this approach can significantly improve the agreement between computed and measured binding energies. When the approach is applied to lactate dehydrogenase A, it can make quantitative predictions about conformational, tautomeric and protonation state preferences as well as stereoselectivity and even identifies potential errors in structures deposited in the Protein Data Bank for this enzyme. By broadening the evidence base for these structures from only the diffraction data, more chemically realistic structures can be proposed.
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Affiliation(s)
- Iva Lukac
- School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Byrom Street , Liverpool , L3 3AF , UK .
| | - Hend Abdelhakim
- School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Byrom Street , Liverpool , L3 3AF , UK .
| | - Richard A Ward
- Chemistry, Oncology, IMED Biotech Unit , AstraZeneca , Cambridge , UK
| | - Stephen A St-Gallay
- Sygnature Discovery Ltd , Bio City, Pennyfoot St , Nottingham , NG1 1GF , UK
| | - Judith C Madden
- School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Byrom Street , Liverpool , L3 3AF , UK .
| | - Andrew G Leach
- School of Pharmacy and Biomolecular Sciences , Liverpool John Moores University , Byrom Street , Liverpool , L3 3AF , UK .
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18
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Thapa HR, Robbins JM, Moore BS, Agarwal V. Insights into Thiotemplated Pyrrole Biosynthesis Gained from the Crystal Structure of Flavin-Dependent Oxidase in Complex with Carrier Protein. Biochemistry 2019; 58:918-929. [PMID: 30620182 DOI: 10.1021/acs.biochem.8b01177] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sequential enzymatic reactions on substrates tethered to carrier proteins (CPs) generate thiotemplated building blocks that are then delivered to nonribosomal peptide synthetases (NRPSs) to generate peptidic natural products. The underlying diversity of these thiotemplated building blocks is the principal driver of the chemical diversity of NRPS-derived natural products. Structural insights into recognition of CPs by tailoring enzymes that generate these building blocks are sparse. Here we present the crystal structure of a flavin-dependent prolyl oxidase that furnishes thiotemplated pyrrole as the product, in complex with its cognate CP in the holo and product-bound states. The thiotemplated pyrrole is an intermediate that is well-represented in natural product biosynthetic pathways. Our results delineate the interactions between the CP and the oxidase while also providing insights into the stereospecificity of the enzymatic oxidation of the prolyl heterocycle to the aromatic pyrrole. Biochemical validation of the interaction between the CP and the oxidase demonstrates that NRPSs recognize and bind to their CPs using interactions quite different from those of fatty acid and polyketide biosynthetic enzymes. Our results posit that structural diversity in natural product biosynthesis can be, and is, derived from subtle modifications of primary metabolic enzymes.
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Affiliation(s)
- Hem R Thapa
- School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - John M Robbins
- School of Chemical and Biomolecular Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.,Krone Engineered Biosystems Building , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Bradley S Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography , University of California, San Diego , La Jolla , California 92093 , United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California, San Diego , La Jolla , California 92093 , United States
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.,School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
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19
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Karkehabadi S, Hansson H, Mikkelsen NE, Kim S, Kaper T, Sandgren M, Gudmundsson M. Structural studies of a glycoside hydrolase family 3 β-glucosidase from the model fungus Neurospora crassa. Acta Crystallogr F Struct Biol Commun 2018; 74:787-796. [PMID: 30511673 PMCID: PMC6277957 DOI: 10.1107/s2053230x18015662] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/05/2018] [Indexed: 11/29/2022] Open
Abstract
The glycoside hydrolase family 3 (GH3) β-glucosidases are a structurally diverse family of enzymes. Cel3A from Neurospora crassa (NcCel3A) belongs to a subfamily of key enzymes that are crucial for industrial biomass degradation. β-Glucosidases hydrolyse the β-1,4 bond at the nonreducing end of cellodextrins. The hydrolysis of cellobiose is of special importance as its accumulation inhibits other cellulases acting on crystalline cellulose. Here, the crystal structure of the biologically relevant dimeric form of NcCel3A is reported. The structure has been refined to 2.25 Å resolution, with an Rcryst and Rfree of 0.18 and 0.22, respectively. NcCel3A is an extensively N-glycosylated glycoprotein that shares 46% sequence identity with Hypocrea jecorina Cel3A, the structure of which has recently been published, and 61% sequence identity with the thermophilic β-glucosidase from Rasamsonia emersonii. NcCel3A is a three-domain protein with a number of extended loops that deepen the active-site cleft of the enzyme. These structures characterize this subfamily of GH3 β-glucosidases and account for the high cellobiose specificity of this subfamily.
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Affiliation(s)
- Saeid Karkehabadi
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Nils Egil Mikkelsen
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Steve Kim
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Thijs Kaper
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Mikael Gudmundsson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
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20
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The laterally acquired GH5 ZgEngA GH5_4 from the marine bacterium Zobellia galactanivorans is dedicated to hemicellulose hydrolysis. Biochem J 2018; 475:3609-3628. [PMID: 30341165 DOI: 10.1042/bcj20180486] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/10/2018] [Accepted: 10/17/2018] [Indexed: 02/01/2023]
Abstract
Cell walls of marine macroalgae are composed of diverse polysaccharides that provide abundant carbon sources for marine heterotrophic bacteria. Among them, Zobellia galactanivorans is considered as a model for studying algae-bacteria interactions. The degradation of typical algal polysaccharides, such as agars or alginate, has been intensively studied in this model bacterium, but the catabolism of plant-like polysaccharides is essentially uncharacterized. Here, we identify a polysaccharide utilization locus in the genome of Z. galactanivorans, induced by laminarin (β-1,3-glucans), and containing a putative GH5 subfamily 4 (GH5_4) enzyme, currently annotated as a endoglucanase (ZgEngAGH5_4). A phylogenetic analysis indicates that ZgEngAGH5_4 was laterally acquired from an ancestral Actinobacteria We performed the biochemical and structural characterization of ZgEngAGH5_4 and demonstrated that this GH5 is, in fact, an endo-β-glucanase, most active on mixed-linked glucan (MLG). Although ZgEngAGH5_4 and GH16 lichenases both hydrolyze MLG, these two types of enzymes release different series of oligosaccharides. Structural analyses of ZgEngAGH5_4 reveal that all the amino acid residues involved in the catalytic triad and in the negative glucose-binding subsites are conserved, when compared with the closest relative, the cellulase EngD from Clostridium cellulovorans, and some other GH5s. In contrast, the positive glucose-binding subsites of ZgEngAGH5_4 are different and this could explain the preference for MLG, with respect to cellulose or laminarin. Molecular dynamics computer simulations using different hexaoses reveal that the specificity for MLG occurs through the +1 and +2 subsites of the binding pocket that display the most important differences when compared with the structures of other GH5_4 enzymes.
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21
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Cramer JT, Führing JI, Baruch P, Brütting C, Knölker HJ, Gerardy-Schahn R, Fedorov R. Decoding Allosteric Networks in Biocatalysts: Rational Approach to Therapies and Biotechnologies. ACS Catal 2018. [DOI: 10.1021/acscatal.7b03714] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Johannes T. Cramer
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
- Institute for Biophysical Chemistry/Research Division for Structural Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Jana I. Führing
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Petra Baruch
- Institute for Biophysical Chemistry/Research Division for Structural Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Christian Brütting
- Department of Chemistry, Technische Universität Dresden, Bergstrasse 66, 01069 Dresden, Germany
| | - Hans-Joachim Knölker
- Department of Chemistry, Technische Universität Dresden, Bergstrasse 66, 01069 Dresden, Germany
| | - Rita Gerardy-Schahn
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
| | - Roman Fedorov
- Institute for Biophysical Chemistry/Research Division for Structural Biochemistry, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany
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22
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DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants. Structure 2018; 26:85-95.e3. [DOI: 10.1016/j.str.2017.11.022] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 10/15/2017] [Accepted: 11/27/2017] [Indexed: 11/20/2022]
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23
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Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities. Structure 2017; 25:1598-1610.e3. [DOI: 10.1016/j.str.2017.07.017] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/20/2017] [Accepted: 07/28/2017] [Indexed: 01/31/2023]
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24
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Elegheert J, Brigé A, Van Beeumen J, Savvides SN. Structural dissection ofShewanella oneidensisold yellow enzyme 4 bound to a Meisenheimer complex and (nitro)phenolic ligands. FEBS Lett 2017; 591:3391-3401. [DOI: 10.1002/1873-3468.12833] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/17/2017] [Accepted: 08/25/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Jonathan Elegheert
- Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE); Department of Biochemistry and Microbiology; Ghent University; Belgium
| | - Ann Brigé
- Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE); Department of Biochemistry and Microbiology; Ghent University; Belgium
- Ablynx NV; Zwijnaarde Belgium
| | - Jozef Van Beeumen
- Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE); Department of Biochemistry and Microbiology; Ghent University; Belgium
| | - Savvas N. Savvides
- Laboratory for Protein Biochemistry and Biomolecular Engineering (L-ProBE); Department of Biochemistry and Microbiology; Ghent University; Belgium
- VIB-UGent Center for Inflammation Research (IRC); Ghent University; Zwijnaarde Belgium
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25
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Sekiguchi Y, Hashimoto S, Kobayashi A, Oroguchi T, Nakasako M. A protocol for searching the most probable phase-retrieved maps in coherent X-ray diffraction imaging by exploiting the relationship between convergence of the retrieved phase and success of calculation. JOURNAL OF SYNCHROTRON RADIATION 2017; 24:1024-1038. [PMID: 28862626 DOI: 10.1107/s1600577517008396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 06/06/2017] [Indexed: 06/07/2023]
Abstract
Coherent X-ray diffraction imaging (CXDI) is a technique for visualizing the structures of non-crystalline particles with size in the submicrometer to micrometer range in material sciences and biology. In the structural analysis of CXDI, the electron density map of a specimen particle projected along the direction of the incident X-rays can be reconstructed only from the diffraction pattern by using phase-retrieval (PR) algorithms. However, in practice, the reconstruction, relying entirely on the computational procedure, sometimes fails because diffraction patterns miss the data in small-angle regions owing to the beam stop and saturation of the detector pixels, and are modified by Poisson noise in X-ray detection. To date, X-ray free-electron lasers have allowed us to collect a large number of diffraction patterns within a short period of time. Therefore, the reconstruction of correct electron density maps is the bottleneck for efficiently conducting structure analyses of non-crystalline particles. To automatically address the correctness of retrieved electron density maps, a data analysis protocol to extract the most probable electron density maps from a set of maps retrieved from 1000 different random seeds for a single diffraction pattern is proposed. Through monitoring the variations of the phase values during PR calculations, the tendency for the PR calculations to succeed when the retrieved phase sets converged on a certain value was found. On the other hand, if the phase set was in persistent variation, the PR calculation tended to fail to yield the correct electron density map. To quantify this tendency, here a figure of merit for the variation of the phase values during PR calculation is introduced. In addition, a PR protocol to evaluate the similarity between a map of the highest figure of merit and other independently reconstructed maps is proposed. The protocol is implemented and practically examined in the structure analyses for diffraction patterns from aggregates of gold colloidal particles. Furthermore, the feasibility of the protocol in the structure analysis of organelles from biological cells is examined.
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Affiliation(s)
- Yuki Sekiguchi
- Department of Physics, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Yokohama, Kohoku, Kanagawa 223-8522, Japan
| | - Saki Hashimoto
- Department of Physics, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Yokohama, Kohoku, Kanagawa 223-8522, Japan
| | - Amane Kobayashi
- Department of Physics, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Yokohama, Kohoku, Kanagawa 223-8522, Japan
| | - Tomotaka Oroguchi
- Department of Physics, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Yokohama, Kohoku, Kanagawa 223-8522, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, Hiyoshi 3-14-1, Yokohama, Kohoku, Kanagawa 223-8522, Japan
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26
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Marion A, Groll M, Scharf DH, Scherlach K, Glaser M, Sievers H, Schuster M, Hertweck C, Brakhage AA, Antes I, Huber EM. Gliotoxin Biosynthesis: Structure, Mechanism, and Metal Promiscuity of Carboxypeptidase GliJ. ACS Chem Biol 2017; 12:1874-1882. [PMID: 28525266 DOI: 10.1021/acschembio.6b00847] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The formation of glutathione (GSH) conjugates, best known from the detoxification of xenobiotics, is a widespread strategy to incorporate sulfur into biomolecules. The biosynthesis of gliotoxin, a virulence factor of the human pathogenic fungus Aspergillus fumigatus, involves attachment of two GSH molecules and their sequential decomposition to yield two reactive thiol groups. The degradation of the GSH moieties requires the activity of the Cys-Gly carboxypeptidase GliJ, for which we describe the X-ray structure here. The enzyme forms a homodimer with each monomer comprising one active site. Two metal ions are present per proteolytic center, thus assigning GliJ to the diverse family of dinuclear metallohydrolases. Depending on availability, Zn2+, Fe2+, Fe3+, Mn2+, Cu2+, Co2+, or Ni2+ ions are accepted as cofactors. Despite this high metal promiscuity, a preference for zinc versus iron and manganese was noted. Mutagenesis experiments revealed details of metal coordination, and molecular modeling delivered insights into substrate recognition and processing by GliJ. The latter results suggest a reaction mechanism in which the two scissile peptide bonds of one gliotoxin precursor molecule are hydrolyzed sequentially and in a given order.
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Affiliation(s)
- Antoine Marion
- Center
for Integrated Protein Science Munich at the Department of Biosciences, Technische Universität München, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany
| | - Michael Groll
- Center
for Integrated Protein Science Munich at the Department Chemistry, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching, Germany
| | - Daniel H. Scharf
- Department
of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), D-07745 Jena, Germany
| | - Kirstin Scherlach
- Department
of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), D-07745 Jena, Germany
| | - Manuel Glaser
- Center
for Integrated Protein Science Munich at the Department of Biosciences, Technische Universität München, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany
| | - Holger Sievers
- Fachgruppe
Analytische Chemie, Technische Universität München, D-85748 Garching, Germany
| | - Michael Schuster
- Fachgruppe
Analytische Chemie, Technische Universität München, D-85748 Garching, Germany
| | - Christian Hertweck
- Department
of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), D-07745 Jena, Germany
- Chair of
Natural Product Chemistry, Friedrich Schiller University (FSU), D-07743 Jena, Germany
| | - Axel A. Brakhage
- Department
of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (HKI), D-07745 Jena, Germany
- Department
of Microbiology and Molecular Biology, Friedrich Schiller University (FSU), D-07743 Jena, Germany
| | - Iris Antes
- Center
for Integrated Protein Science Munich at the Department of Biosciences, Technische Universität München, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany
| | - Eva M. Huber
- Center
for Integrated Protein Science Munich at the Department Chemistry, Technische Universität München, Lichtenbergstr. 4, D-85748 Garching, Germany
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27
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van Roon AMM, Oubridge C, Obayashi E, Sposito B, Newman AJ, Séraphin B, Nagai K. Crystal structure of U2 snRNP SF3b components: Hsh49p in complex with Cus1p-binding domain. RNA (NEW YORK, N.Y.) 2017; 23:968-981. [PMID: 28348170 PMCID: PMC5435868 DOI: 10.1261/rna.059378.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 03/17/2017] [Indexed: 05/02/2023]
Abstract
Spliceosomal proteins Hsh49p and Cus1p are components of SF3b, which together with SF3a, Msl1p/Lea1p, Sm proteins, and U2 snRNA, form U2 snRNP, which plays a crucial role in pre-mRNA splicing. Hsh49p, comprising two RRMs, forms a heterodimer with Cus1p. We determined the crystal structures of Saccharomyces cerevisiae full-length Hsh49p as well as its RRM1 in complex with a minimal binding region of Cus1p (residues 290-368). The structures show that the Cus1 fragment binds to the α-helical surface of Hsh49p RRM1, opposite the four-stranded β-sheet, leaving the canonical RNA-binding surface available to bind RNA. Hsh49p binds the 5' end region of U2 snRNA via RRM1. Its affinity is increased in complex with Cus1(290-368)p, partly because an extended RNA-binding surface forms across the protein-protein interface. The Hsh49p RRM1-Cus1(290-368)p structure fits well into cryo-EM density of the Bact spliceosome, corroborating the biological relevance of our crystal structure.
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Affiliation(s)
| | - Chris Oubridge
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Eiji Obayashi
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Benedetta Sposito
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Bertrand Séraphin
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé et de la Recherche Médicale (INSERM), U964/Université de Strasbourg, 67404 Illkirch, France
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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28
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Xu C, Ishikawa H, Izumikawa K, Li L, He H, Nobe Y, Yamauchi Y, Shahjee HM, Wu XH, Yu YT, Isobe T, Takahashi N, Min J. Structural insights into Gemin5-guided selection of pre-snRNAs for snRNP assembly. Genes Dev 2016; 30:2376-2390. [PMID: 27881600 PMCID: PMC5131778 DOI: 10.1101/gad.288340.116] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/26/2016] [Indexed: 12/26/2022]
Abstract
Xu et al. show that the WD40 domain of Gemin5 is both necessary and sufficient for binding the Sm site of pre-snRNAs. They also determined the crystal structures of the WD40 domain of Gemin5 in complex with the Sm site or m7G cap of pre-snRNA. In cytoplasm, the survival of motor neuron (SMN) complex delivers pre-small nuclear RNAs (pre-snRNAs) to the heptameric Sm ring for the assembly of the ring complex on pre-snRNAs at the conserved Sm site [A(U)4–6G]. Gemin5, a WD40 protein component of the SMN complex, is responsible for recognizing pre-snRNAs. In addition, Gemin5 has been reported to specifically bind to the m7G cap. In this study, we show that the WD40 domain of Gemin5 is both necessary and sufficient for binding the Sm site of pre-snRNAs by isothermal titration calorimetry (ITC) and mutagenesis assays. We further determined the crystal structures of the WD40 domain of Gemin5 in complex with the Sm site or m7G cap of pre-snRNA, which reveal that the WD40 domain of Gemin5 recognizes the Sm site and m7G cap of pre-snRNAs via two distinct binding sites by respective base-specific interactions. In addition, we also uncovered a novel role of Gemin5 in escorting the truncated forms of U1 pre-snRNAs for proper disposal. Overall, the elucidated Gemin5 structures will contribute to a better understanding of Gemin5 in small nuclear ribonucleic protein (snRNP) biogenesis as well as, potentially, other cellular activities.
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Affiliation(s)
- Chao Xu
- Hefei National Laboratory for Physical Sciences at Microscale, Hefei Science Center of CAS, Chinese Academy of Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Hideaki Ishikawa
- Department of Applied Biological Science, Graduate School of Agriculture and Global Innovation Research Organization, Tokyo University of Agriculture and Technology, Fuchu-Shi, Tokyo 183-8509, Japan
| | - Keiichi Izumikawa
- Department of Applied Biological Science, Graduate School of Agriculture and Global Innovation Research Organization, Tokyo University of Agriculture and Technology, Fuchu-Shi, Tokyo 183-8509, Japan
| | - Li Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Hao He
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Yuko Nobe
- Department of Chemistry, Tokyo Metropolitan University, Hachiouji-shi, Tokyo 192-0397, Japan
| | - Yoshio Yamauchi
- Department of Chemistry, Tokyo Metropolitan University, Hachiouji-shi, Tokyo 192-0397, Japan
| | - Hanief M Shahjee
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Xian-Hui Wu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Toshiaki Isobe
- Department of Chemistry, Tokyo Metropolitan University, Hachiouji-shi, Tokyo 192-0397, Japan
| | - Nobuhiro Takahashi
- Department of Applied Biological Science, Graduate School of Agriculture and Global Innovation Research Organization, Tokyo University of Agriculture and Technology, Fuchu-Shi, Tokyo 183-8509, Japan
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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29
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Butler KV, Ma A, Yu W, Li F, Tempel W, Babault N, Pittella-Silva F, Shao J, Wang J, Luo M, Vedadi M, Brown PJ, Arrowsmith CH, Jin J. Structure-Based Design of a Covalent Inhibitor of the SET Domain-Containing Protein 8 (SETD8) Lysine Methyltransferase. J Med Chem 2016; 59:9881-9889. [PMID: 27804297 DOI: 10.1021/acs.jmedchem.6b01244] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Selective inhibitors of protein lysine methyltransferases, including SET domain-containing protein 8 (SETD8), are highly desired, as only a fraction of these enzymes are associated with high-quality inhibitors. From our previously discovered SETD8 inhibitor, we developed a more potent analog and solved a cocrystal structure, which is the first crystal structure of SETD8 in complex with a small-molecule inhibitor. This cocrystal structure allowed the design of a covalent inhibitor of SETD8 (MS453), which specifically modifies a cysteine residue near the inhibitor binding site, has an IC50 value of 804 nM, reacts with SETD8 with near-quantitative yield, and is selective for SETD8 against 28 other methyltransferases. We also solved the crystal structure of the covalent inhibitor in complex with SETD8. This work provides atomic-level perspective on the inhibition of SETD8 by small molecules and will help identify high-quality chemical probes of SETD8.
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Affiliation(s)
- Kyle V Butler
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Anqi Ma
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Wenyu Yu
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Nicolas Babault
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Fabio Pittella-Silva
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Jason Shao
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Junyi Wang
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Minkui Luo
- Molecular Pharmacology and Chemistry Program, Memorial Sloan Kettering Cancer Center , New York, New York 10065, United States
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto , Toronto, Ontario M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Jian Jin
- Department of Pharmacological Sciences and Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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30
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Matsunami H, Yoon YH, Meshcheryakov VA, Namba K, Samatey FA. Structural flexibility of the periplasmic protein, FlgA, regulates flagellar P-ring assembly in Salmonella enterica. Sci Rep 2016; 6:27399. [PMID: 27273476 PMCID: PMC4895218 DOI: 10.1038/srep27399] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 05/18/2016] [Indexed: 11/21/2022] Open
Abstract
A periplasmic flagellar chaperone protein, FlgA, is required for P-ring assembly in bacterial flagella of taxa such as Salmonella enterica or Escherichia coli. The mechanism of chaperone-mediated P-ring formation is poorly understood. Here we present the open and closed crystal structures of FlgA from Salmonella enterica serovar Typhimurium, grown under different crystallization conditions. An intramolecular disulfide cross-linked form of FlgA caused a dominant negative effect on motility of the wild-type strain. Pull-down experiments support a specific protein-protein interaction between FlgI, the P-ring component protein, and the C-terminal domain of FlgA. Surface plasmon resonance and limited-proteolysis indicate that flexibility of the domain is reduced in the covalently closed form. These results show that the structural flexibility of the C-terminal domain of FlgA, which is related to the structural difference between the two crystal forms, is intrinsically associated with its molecular chaperone function in P-ring assembly.
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Affiliation(s)
- Hideyuki Matsunami
- Trans-Membrane Trafficking Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami, Okinawa 904-0495, Japan
| | - Young-Ho Yoon
- Trans-Membrane Trafficking Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami, Okinawa 904-0495, Japan
| | - Vladimir A Meshcheryakov
- Trans-Membrane Trafficking Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami, Okinawa 904-0495, Japan
| | - Keiichi Namba
- Dynamic NanoM achine Project, International Cooperative Research Project, Japan Science and Technology Agency, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.,Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.,Riken Quantitative Biology Center, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Fadel A Samatey
- Trans-Membrane Trafficking Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Kunigami, Okinawa 904-0495, Japan
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31
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Duell ER, Glaser M, Le Chapelain C, Antes I, Groll M, Huber EM. Sequential Inactivation of Gliotoxin by the S-Methyltransferase TmtA. ACS Chem Biol 2016; 11:1082-9. [PMID: 26808594 DOI: 10.1021/acschembio.5b00905] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The epipolythiodioxopiperazine (ETP) gliotoxin mediates toxicity via its reactive thiol groups and thereby contributes to virulence of the human pathogenic fungus Aspergillus fumigatus. Self-intoxication of the mold is prevented either by reversible oxidation of reduced gliotoxin or by irreversible conversion to bis(methylthio)gliotoxin. The latter is produced by the S-methyltransferase TmtA and attenuates ETP biosynthesis. Here, we report the crystal structure of TmtA in complex with S-(5'-adenosyl)-l-homocysteine. TmtA features one substrate and one cofactor binding pocket per protein, and thus, bis-thiomethylation of gliotoxin occurs sequentially. Molecular docking of substrates and products into the active site of TmtA reveals that gliotoxin forms specific interactions with the protein surroundings, and free energy calculations indicate that methylation of the C10a-SH group precedes alkylation of the C3-SH site. Altogether, TmtA is well suited to selectively convert gliotoxin and to control its biosynthesis, suggesting that homologous enzymes serve to regulate the production of their toxic natural sulfur compounds in a similar manner.
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Affiliation(s)
- Elke R. Duell
- Center for Integrated Protein
Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Manuel Glaser
- Center for Integrated Protein
Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Camille Le Chapelain
- Center for Integrated Protein
Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Iris Antes
- Center for Integrated Protein
Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Michael Groll
- Center for Integrated Protein
Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Eva M. Huber
- Center for Integrated Protein
Science Munich (CIPSM) at the Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
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32
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Alkire RW, Rotella FJ, Duke NEC, Otwinowski Z, Borek D. Taking a look at the calibration of a CCD detector with a fiber-optic taper. J Appl Crystallogr 2016; 49:415-425. [PMID: 27047303 DOI: 10.1107/s1600576716000431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 01/08/2016] [Indexed: 11/11/2022] Open
Abstract
At the Structural Biology Center beamline 19BM, located at the Advanced Photon Source, the operational characteristics of the equipment are routinely checked to ensure they are in proper working order. After performing a partial flat-field calibration for the ADSC Quantum 210r CCD detector, it was confirmed that the detector operates within specifications. However, as a secondary check it was decided to scan a single reflection across one-half of a detector module to validate the accuracy of the calibration. The intensities from this single reflection varied by more than 30% from the module center to the corner of the module. Redistribution of light within bent fibers of the fiber-optic taper was identified to be a source of this variation. The degree to which the diffraction intensities are corrected to account for characteristics of the fiber-optic tapers depends primarily upon the experimental strategy of data collection, approximations made by the data processing software during scaling, and crystal symmetry.
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Affiliation(s)
- R W Alkire
- Biosciences Division, Argonne National Laboratory , 9700 S. Cass Avenue, Argonne, Illinois 60439, USA
| | - F J Rotella
- Biosciences Division, Argonne National Laboratory , 9700 S. Cass Avenue, Argonne, Illinois 60439, USA
| | - N E C Duke
- Biosciences Division, Argonne National Laboratory , 9700 S. Cass Avenue, Argonne, Illinois 60439, USA
| | - Zbyszek Otwinowski
- Department of Biophysics, University of Texas Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Dominika Borek
- Department of Biophysics, University of Texas Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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Liu Y, Tempel W, Zhang Q, Liang X, Loppnau P, Qin S, Min J. Family-wide Characterization of Histone Binding Abilities of Human CW Domain-containing Proteins. J Biol Chem 2016; 291:9000-13. [PMID: 26933034 DOI: 10.1074/jbc.m116.718973] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Indexed: 01/08/2023] Open
Abstract
Covalent modifications of histone N-terminal tails play a critical role in regulating chromatin structure and controlling gene expression. These modifications are controlled by histone-modifying enzymes and read out by histone-binding proteins. Numerous proteins have been identified as histone modification readers. Here we report the family-wide characterization of histone binding abilities of human CW domain-containing proteins. We demonstrate that the CW domains in ZCWPW2 and MORC3/4 selectively recognize histone H3 trimethylated at Lys-4, similar to ZCWPW1 reported previously, while the MORC1/2 and LSD2 lack histone H3 Lys-4 binding ability. Our crystal structures of the CW domains of ZCWPW2 and MORC3 in complex with the histone H3 trimethylated at Lys-4 peptide reveal the molecular basis of this interaction. In each complex, two tryptophan residues in the CW domain form the "floor" and "right wall," respectively, of the methyllysine recognition cage. Our mutation results based on ZCWPW2 reveal that the right wall tryptophan residue is essential for binding, and the floor tryptophan residue enhances binding affinity. Our structural and mutational analysis highlights the conserved roles of the cage residues of CW domain across the histone methyllysine binders but also suggests why some CW domains lack histone binding ability.
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Affiliation(s)
- Yanli Liu
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, the Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, China
| | - Wolfram Tempel
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Qi Zhang
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Xiao Liang
- the Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, China
| | - Peter Loppnau
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Su Qin
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, the Life Science Research Center, South University of Science and Technology of China, Shenzhen 518055, China, and
| | - Jinrong Min
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, the Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, China, the Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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Sekiguchi Y, Oroguchi T, Nakasako M. Classification and assessment of retrieved electron density maps in coherent X-ray diffraction imaging using multivariate analysis. JOURNAL OF SYNCHROTRON RADIATION 2016; 23:312-323. [PMID: 26698079 DOI: 10.1107/s1600577515018202] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/29/2015] [Indexed: 06/05/2023]
Abstract
Coherent X-ray diffraction imaging (CXDI) is one of the techniques used to visualize structures of non-crystalline particles of micrometer to submicrometer size from materials and biological science. In the structural analysis of CXDI, the electron density map of a sample particle can theoretically be reconstructed from a diffraction pattern by using phase-retrieval (PR) algorithms. However, in practice, the reconstruction is difficult because diffraction patterns are affected by Poisson noise and miss data in small-angle regions due to the beam stop and the saturation of detector pixels. In contrast to X-ray protein crystallography, in which the phases of diffracted waves are experimentally estimated, phase retrieval in CXDI relies entirely on the computational procedure driven by the PR algorithms. Thus, objective criteria and methods to assess the accuracy of retrieved electron density maps are necessary in addition to conventional parameters monitoring the convergence of PR calculations. Here, a data analysis scheme, named ASURA, is proposed which selects the most probable electron density maps from a set of maps retrieved from 1000 different random seeds for a diffraction pattern. Each electron density map composed of J pixels is expressed as a point in a J-dimensional space. Principal component analysis is applied to describe characteristics in the distribution of the maps in the J-dimensional space. When the distribution is characterized by a small number of principal components, the distribution is classified using the k-means clustering method. The classified maps are evaluated by several parameters to assess the quality of the maps. Using the proposed scheme, structure analysis of a diffraction pattern from a non-crystalline particle is conducted in two stages: estimation of the overall shape and determination of the fine structure inside the support shape. In each stage, the most accurate and probable density maps are objectively selected. The validity of the proposed scheme is examined by application to diffraction data that were obtained from an aggregate of metal particles and a biological specimen at the XFEL facility SACLA using custom-made diffraction apparatus.
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Affiliation(s)
- Yuki Sekiguchi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Tomotaka Oroguchi
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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Structural basis for the regulatory role of the PPxY motifs in the thioredoxin-interacting protein TXNIP. Biochem J 2015; 473:179-87. [PMID: 26527736 DOI: 10.1042/bj20150830] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/02/2015] [Indexed: 11/17/2022]
Abstract
TXNIP (thioredoxin-interacting protein) negatively regulates the antioxidative activity of thioredoxin and participates in pleiotropic cellular processes. Its deregulation is linked to various human diseases, including diabetes, acute myeloid leukaemia and cardiovascular diseases. The E3 ubiquitin ligase Itch (Itchy homologue) polyubiquitinates TXNIP to promote its degradation via the ubiquitin-proteasome pathway, and this Itch-mediated polyubiquitination of TXNIP is dependent on the interaction of the four WW domains of Itch with the two PPxY motifs of TXNIP. However, the molecular mechanism of this interaction of TXNIP with Itch remains elusive. In the present study, we found that each of the four WW domains of Itch exhibited different binding affinities for TXNIP, whereas multivalent engagement between the four WW domains of Itch and the two PPxY motifs of TXNIP resulted in their strong binding avidity. Our structural analyses demonstrated that the third and fourth WW domains of Itch were able to recognize both PPxY motifs of TXNIP simultaneously, supporting a multivalent binding mode between Itch and TXNIP. Interestingly, the phosphorylation status on the tyrosine residue of the PPxY motifs of TXNIP serves as a molecular switch in its choice of binding partners and thereby downstream biological signalling outcomes. Phosphorylation of this tyrosine residue of TXNIP diminished the binding capability of PPxY motifs of TXNIP to Itch, whereas this phosphorylation is a prerequisite to the binding activity of TXNIP to SHP2 [SH2 (Src homology 2) domain-containing protein tyrosine phosphatase 2] and their roles in stabilizing the phosphorylation and activation of CSK (c-Src tyrosine kinase).
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Crystal structural basis for Rv0315, an immunostimulatory antigen and inactive beta-1,3-glucanase of Mycobacterium tuberculosis. Sci Rep 2015; 5:15073. [PMID: 26469317 PMCID: PMC4606783 DOI: 10.1038/srep15073] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 09/15/2015] [Indexed: 11/30/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) remains a leading cause of morbidity and mortality worldwide, as two billion people are latently infected with Mtb. To address Mtb drug resistance and the limitations of current vaccines, the characteristics of candidate Mtb vaccines need to be explored. Here, we report the three-dimensional structure of Rv0315 at 1.70 Å resolution, a novel immunostimulatory antigen of Mtb, and demonstrate that Rv0315 is an inactive β-1,3-glucanase of the glycoside hydrolase 16 (GH16) family. Our study further elaborates the molecular basis for the lack of glucan recognition by Rv0315. Rv0315 has a large open groove, and this particular topology cannot bind oligosaccharide chains in solution, thus explaining the lack of detectable hydrolytic activity towards its substrate. Additionally, we identified Glu-176, a conserved catalytic residue in GH16 endo-β-1,3-glucanases, as essential for Rv0315 to induce immunological responses. These results indicate that Rv0315 likely diverged from a broad-specificity ancestral GH16 glucanase, and this inactive member of the GH16 family offers new insights into the GH16 glucanase. Together, our findings suggest that an inactive β-1,3-glucanase in Mtb drives T-helper 1 (Th1) immune responses, which may help develop more effective vaccines against Mtb infection.
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37
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Crystal structure of human nuclear pore complex component NUP43. FEBS Lett 2015; 589:3247-53. [DOI: 10.1016/j.febslet.2015.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 08/29/2015] [Accepted: 09/08/2015] [Indexed: 01/10/2023]
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38
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Han Q, Zhou C, Wu S, Liu Y, Triplett L, Miao J, Tokuhisa J, Deblais L, Robinson H, Leach JE, Li J, Zhao B. Crystal Structure of Xanthomonas AvrRxo1-ORF1, a Type III Effector with a Polynucleotide Kinase Domain, and Its Interactor AvrRxo1-ORF2. Structure 2015; 23:1900-1909. [PMID: 26344722 DOI: 10.1016/j.str.2015.06.030] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Revised: 05/19/2015] [Accepted: 06/30/2015] [Indexed: 12/27/2022]
Abstract
Xanthomonas oryzae pv. oryzicola (Xoc) causes bacterial leaf streak (BLS) disease on rice plants. Xoc delivers a type III effector AvrRxo1-ORF1 into rice plant cells that can be recognized by disease resistance (R) protein Rxo1, and triggers resistance to BLS disease. However, the mechanism and virulence role of AvrRxo1 is not known. In the genome of Xoc, AvrRxo1-ORF1 is adjacent to another gene AvrRxo1-ORF2, which was predicted to encode a molecular chaperone of AvrRxo1-ORF1. We report the co-purification and crystallization of the AvrRxo1-ORF1:AvrRxo1-ORF2 tetramer complex at 1.64 Å resolution. AvrRxo1-ORF1 has a T4 polynucleotide kinase domain, and expression of AvrRxo1-ORF1 suppresses bacterial growth in a manner dependent on the kinase motif. Although AvrRxo1-ORF2 binds AvrRxo1-ORF1, it is structurally different from typical effector-binding chaperones, in that it has a distinct fold containing a novel kinase-binding domain. AvrRxo1-ORF2 functions to suppress the bacteriostatic activity of AvrRxo1-ORF1 in bacterial cells.
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Affiliation(s)
- Qian Han
- Laboratory of Tropical Veterinary Medicine and Vector Biology, and Hainan Key Laboratory of Sustainable Utilization of Tropical Bioresources, College of Agriculture, Hainan University, Haikou 570228, Hainan, China; Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Changhe Zhou
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061, USA
| | - Shuchi Wu
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061, USA
| | - Yi Liu
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061, USA
| | - Lindsay Triplett
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Jiamin Miao
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061, USA
| | - James Tokuhisa
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061, USA
| | - Loïc Deblais
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Howard Robinson
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jan E Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Jianyong Li
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061, USA.
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Xu C, Liu K, Ahmed H, Loppnau P, Schapira M, Min J. Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins. J Biol Chem 2015; 290:24902-13. [PMID: 26318451 DOI: 10.1074/jbc.m115.680389] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Indexed: 11/06/2022] Open
Abstract
N(6)-Methyladenosine (m(6)A) is the most abundant internal modification in RNA and is specifically recognized by YT521-B homology (YTH) domain-containing proteins. Recently we reported that YTHDC1 prefers guanosine and disfavors adenosine at the position preceding the m(6)A nucleotide in RNA and preferentially binds to the GG(m(6)A)C sequence. Now we systematically characterized the binding affinities of the YTH domains of three other human proteins and yeast YTH domain protein Pho92 and determined the crystal structures of the YTH domains of human YTHDF1 and yeast Pho92 in complex with a 5-mer m(6)A RNA, respectively. Our binding and structural data revealed that the YTH domain used a conserved aromatic cage to recognize m(6)A. Nevertheless, none of these YTH domains, except YTHDC1, display sequence selectivity at the position preceding the m(6)A modification. Structural comparison of these different YTH domains revealed that among those, only YTHDC1 harbors a distinctly selective binding pocket for the nucleotide preceding the m(6)A nucleotide.
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Affiliation(s)
- Chao Xu
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7 and
| | - Ke Liu
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7 and
| | - Hazem Ahmed
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7 and
| | - Peter Loppnau
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7 and
| | - Matthieu Schapira
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7 and
| | - Jinrong Min
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7 and the Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8 Canada
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40
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Weichenberger CX, Afonine PV, Kantardjieff K, Rupp B. The solvent component of macromolecular crystals. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1023-38. [PMID: 25945568 PMCID: PMC4427195 DOI: 10.1107/s1399004715006045] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 03/25/2015] [Indexed: 11/10/2022]
Abstract
The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initial phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.
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Affiliation(s)
- Christian X. Weichenberger
- Center for Biomedicine, European Academy of Bozen/Bolzano (EURAC), Viale Druso 1, Bozen/Bolzano, I-39100 Südtirol/Alto Adige, Italy
| | - Pavel V. Afonine
- Physical Biosciences Division, Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Mail Stop 64R0121, Berkeley, CA 94720, USA
| | - Katherine Kantardjieff
- College of Science and Mathematics, California State University, San Marcos, CA 92078, USA
| | - Bernhard Rupp
- Department of Forensic Crystallography, k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084, USA
- Department of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck, Austria
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Afonine PV, Moriarty NW, Mustyakimov M, Sobolev OV, Terwilliger TC, Turk D, Urzhumtsev A, Adams PD. FEM: feature-enhanced map. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:646-66. [PMID: 25760612 PMCID: PMC4356370 DOI: 10.1107/s1399004714028132] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 12/25/2014] [Indexed: 11/29/2022]
Abstract
A method is presented that modifies a 2mFobs - DFmodel σA-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the starting map and filling in missing reflections using multiple methods. This is followed by restricting the map to regions with convincing density and the application of sharpening. The final map is then created by combining a series of histogram-equalized intermediate maps. In the test cases shown, the maps produced in this way are found to have increased interpretability and decreased model bias compared with the starting 2mFobs - DFmodel σA-weighted map.
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Affiliation(s)
- Pavel V. Afonine
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA
| | - Nigel W. Moriarty
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA
| | - Marat Mustyakimov
- Biology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA
| | - Oleg V. Sobolev
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA
| | | | - Dusan Turk
- Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Alexandre Urzhumtsev
- Centre for Integrative Biology, IGBMC, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France
- Département de Physique, Faculté des Sciences et des Technologies, Université de Lorraine, 54506 Vandoeuvre-lès-Nancy, France
| | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
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Bunkóczi G, McCoy AJ, Echols N, Grosse-Kunstleve RW, Adams PD, Holton JM, Read RJ, Terwilliger TC. Macromolecular X-ray structure determination using weak, single-wavelength anomalous data. Nat Methods 2015; 12:127-30. [PMID: 25532136 PMCID: PMC4312553 DOI: 10.1038/nmeth.3212] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 11/11/2014] [Indexed: 01/09/2023]
Abstract
We describe a likelihood-based method for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by single-wavelength anomalous diffraction (SAD) X-ray analysis with weak anomalous signal. With the use of partial models and electron density maps in searches for anomalously scattering atoms, testing of alternative values of parameters and parallelized automated model-building, this method has the potential to extend the applicability of the SAD method in challenging cases.
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Affiliation(s)
- Gábor Bunkóczi
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Airlie J. McCoy
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
| | - Nathaniel Echols
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Ralf W. Grosse-Kunstleve
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - Paul D. Adams
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
| | - James M. Holton
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720-8235, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Randy J. Read
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England
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The Vanadium Iodoperoxidase from the marine flavobacteriaceae species Zobellia galactanivorans reveals novel molecular and evolutionary features of halide specificity in the vanadium haloperoxidase enzyme family. Appl Environ Microbiol 2014; 80:7561-73. [PMID: 25261522 DOI: 10.1128/aem.02430-14] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Vanadium haloperoxidases (VHPO) are key enzymes that oxidize halides and are involved in the biosynthesis of organo-halogens. Until now, only chloroperoxidases (VCPO) and bromoperoxidases (VBPO) have been characterized structurally, mainly from eukaryotic species. Three putative VHPO genes were predicted in the genome of the flavobacterium Zobellia galactanivorans, a marine bacterium associated with macroalgae. In a phylogenetic analysis, these putative bacterial VHPO were closely related to other VHPO from diverse bacterial phyla but clustered independently from eukaryotic algal VBPO and fungal VCPO. Two of these bacterial VHPO, heterogeneously produced in Escherichia coli, were found to be strictly specific for iodide oxidation. The crystal structure of one of these vanadium-dependent iodoperoxidases, Zg-VIPO1, was solved by multiwavelength anomalous diffraction at 1.8 Å, revealing a monomeric structure mainly folded into α-helices. This three-dimensional structure is relatively similar to those of VCPO of the fungus Curvularia inaequalis and of Streptomyces sp. and is superimposable onto the dimeric structure of algal VBPO. Surprisingly, the vanadate binding site of Zg-VIPO1 is strictly conserved with the fungal VCPO active site. Using site-directed mutagenesis, we showed that specific amino acids and the associated hydrogen bonding network around the vanadate center are essential for the catalytic properties and also the iodide specificity of Zg-VIPO1. Altogether, phylogeny and structure-function data support the finding that iodoperoxidase activities evolved independently in bacterial and algal lineages, and this sheds light on the evolution of the VHPO enzyme family.
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44
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Chen CD, Huang YC, Chiang HL, Hsieh YC, Guan HH, Chuankhayan P, Chen CJ. Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density and ab initio structure determination. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2331-43. [PMID: 25195747 PMCID: PMC4157445 DOI: 10.1107/s1399004714013868] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 06/13/2014] [Indexed: 11/10/2022]
Abstract
Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron-density modification, model building and structure determination of biological macromolecules using the single-wavelength anomalous dispersion (SAD) method. Two possible phase solutions (φ1 and φ2) generated from two symmetric phase triangles in the Harker construction for the SAD method cause the well known phase ambiguity. A novel direct phase-selection method utilizing the θ(DS) list as a criterion to select optimized phases φ(am) from φ1 or φ2 of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases φ(SAD) has been developed. Based on this work, reflections with an angle θ(DS) in the range 35-145° are selected for an optimized improvement, where θ(DS) is the angle between the initial phase φ(SAD) and a preliminary density-modification (DM) phase φ(DM)(NHL). The results show that utilizing the additional direct phase-selection step prior to simple solvent flattening without phase combination using existing DM programs, such as RESOLVE or DM from CCP4, significantly improves the final phases in terms of increased correlation coefficients of electron-density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase-selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination.
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Affiliation(s)
- Chung-De Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
| | - Yen-Chieh Huang
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
| | - Hsin-Lin Chiang
- Department of Physics, National Tsing Hua University, Hsinchu, Taiwan
| | - Yin-Cheng Hsieh
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
| | - Hong-Hsiang Guan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
| | - Phimonphan Chuankhayan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
| | - Chun-Jung Chen
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu 30076, Taiwan
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45
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Karkehabadi S, Helmich KE, Kaper T, Hansson H, Mikkelsen NE, Gudmundsson M, Piens K, Fujdala M, Banerjee G, Scott-Craig JS, Walton JD, Phillips GN, Sandgren M. Biochemical characterization and crystal structures of a fungal family 3 β-glucosidase, Cel3A from Hypocrea jecorina. J Biol Chem 2014; 289:31624-37. [PMID: 25164811 DOI: 10.1074/jbc.m114.587766] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cellulase mixtures from Hypocrea jecorina are commonly used for the saccharification of cellulose in biotechnical applications. The most abundant β-glucosidase in the mesophilic fungus Hypocrea jecorina is HjCel3A, which hydrolyzes the β-linkage between two adjacent molecules in dimers and short oligomers of glucose. It has been shown that enhanced levels of HjCel3A in H. jecorina cellulase mixtures benefit the conversion of cellulose to glucose. Biochemical characterization of HjCel3A shows that the enzyme efficiently hydrolyzes (1,4)- as well as (1,2)-, (1,3)-, and (1,6)-β-D-linked disaccharides. For crystallization studies, HjCel3A was produced in both H. jecorina (HjCel3A) and Pichia pastoris (Pp-HjCel3A). Whereas the thermostabilities of HjCel3A and Pp-HjCel3A are the same, Pp-HjCel3A has a higher degree of N-linked glycosylation. Here, we present x-ray structures of HjCel3A with and without glucose bound in the active site. The structures have a three-domain architecture as observed previously for other glycoside hydrolase family 3 β-glucosidases. Both production hosts resulted in HjCel3A structures that have N-linked glycosylations at Asn(208) and Asn(310). In H. jecorina-produced HjCel3A, a single N-acetylglucosamine is present at both sites, whereas in Pp-HjCel3A, the P. pastoris-produced HjCel3A enzyme, the glycan chains consist of 8 or 4 saccharides. The glycosylations are involved in intermolecular contacts in the structures derived from either host. Due to the different sizes of the glycosylations, the interactions result in different crystal forms for the two protein forms.
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Affiliation(s)
- Saeid Karkehabadi
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Kate E Helmich
- the Department of Energy Great Lakes Bioenergy Research Center and Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Thijs Kaper
- DuPont Industrial Biosciences, Palo Alto, California 94304
| | - Henrik Hansson
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Nils-Egil Mikkelsen
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Mikael Gudmundsson
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Kathleen Piens
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | | | - Goutami Banerjee
- the Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824, and
| | - John S Scott-Craig
- the Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824, and
| | - Jonathan D Walton
- the Department of Energy Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan 48824, and
| | - George N Phillips
- the Department of Energy Great Lakes Bioenergy Research Center and Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, the Department of Biochemistry and Cell Biology and Department of Chemistry, Rice University, Houston, Texas 77251
| | - Mats Sandgren
- From the Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden,
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46
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Rodrigue J, Ganne G, Blanchard B, Saucier C, Giguère D, Shiao TC, Varrot A, Imberty A, Roy R. Aromatic thioglycoside inhibitors against the virulence factor LecA from Pseudomonas aeruginosa. Org Biomol Chem 2014; 11:6906-18. [PMID: 24057051 DOI: 10.1039/c3ob41422a] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Three small families of hydrolytically stable thioaryl glycosides were prepared as inhibitors of the LecA (PA-IL) virulence factor corresponding to the carbohydrate binding lectin from the bacterial pathogen Pseudomonas aeruginosa. The monosaccharidic arylthio β-d-galactopyranosides served as a common template for the major series that was also substituted at the O-3 position. Arylthio disaccharides from lactose and from melibiose constituted the other two series members. In spite of the fact that the natural ligand for LecA is a glycolipid of the globotriaosylceramide having an α-d-galactopyranoside epitope, this study illustrated that the β-d-galactopyranoside configuration having a hydrophobic aglycon could override the requirement toward the anomeric configuration of the natural sugar. The enzyme linked lectin assay together with isothermal titration microcalorimetry established that naphthyl 1-thio-β-d-galactopyranoside () gave the best inhibition with an IC50 twenty-three times better than that of the reference methyl α-d-galactopyranoside. In addition it showed a KD of 6.3 μM which was ten times better than that of the reference compound. The X-ray crystal structure of LecA with was also obtained.
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Affiliation(s)
- Jacques Rodrigue
- PharmaQAM - Department of Chemistry, Université du Québec à Montréal, P.O. Box 8888, Succ. Centre-ville, Montréal, Québec, Canada H3C 3P8.
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47
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Stemberk V, Jones RPO, Moroz O, Atkin KE, Edwards AM, Turkenburg JP, Leech AP, Massey RC, Potts JR. Evidence for steric regulation of fibrinogen binding to Staphylococcus aureus fibronectin-binding protein A (FnBPA). J Biol Chem 2014; 289:12842-51. [PMID: 24627488 PMCID: PMC4007472 DOI: 10.1074/jbc.m113.543546] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The adjacent fibrinogen (Fg)- and fibronectin (Fn)-binding sites on Fn-binding protein A (FnBPA), a cell surface protein from Staphylococcus aureus, are implicated in the initiation and persistence of infection. FnBPA contains a single Fg-binding site (that also binds elastin) and multiple Fn-binding sites. Here, we solved the structure of the N2N3 domains containing the Fg-binding site of FnBPA in the apo form and in complex with a Fg peptide. The Fg binding mechanism is similar to that of homologous bacterial proteins but without the requirement for "latch" strand residues. We show that the Fg-binding sites and the most N-terminal Fn-binding sites are nonoverlapping but in close proximity. Although Fg and a subdomain of Fn can form a ternary complex on an FnBPA protein construct containing a Fg-binding site and single Fn-binding site, binding of intact Fn appears to inhibit Fg binding, suggesting steric regulation. Given the concentrations of Fn and Fg in the plasma, this mechanism might result in targeting of S. aureus to fibrin-rich thrombi or elastin-rich tissues.
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Affiliation(s)
| | | | - Olga Moroz
- Chemistry, University of York, York YO10 5DD, United Kingdom and
| | | | - Andrew M. Edwards
- the Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | | | | | - Ruth C. Massey
- the Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Jennifer R. Potts
- From the Departments of Biology and , Recipient of British Heart Foundation Senior Basic Science Research Fellowship FS/12/36/29588. To whom correspondence should be addressed. Tel.: 44-1904-328679; E-mail:
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48
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Collén PN, Jeudy A, Sassi JF, Groisillier A, Czjzek M, Coutinho PM, Helbert W. A novel unsaturated β-glucuronyl hydrolase involved in ulvan degradation unveils the versatility of stereochemistry requirements in family GH105. J Biol Chem 2014; 289:6199-211. [PMID: 24407291 DOI: 10.1074/jbc.m113.537480] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ulvans are cell wall matrix polysaccharides in green algae belonging to the genus Ulva. Enzymatic degradation of the polysaccharide by ulvan lyases leads to the production of oligosaccharides with an unsaturated β-glucuronyl residue located at the non-reducing end. Exploration of the genomic environment around the Nonlabens ulvanivorans (previously Percicivirga ulvanivorans) ulvan lyase revealed a gene highly similar to known unsaturated uronyl hydrolases classified in the CAZy glycoside hydrolase family 105. The gene was cloned, the protein was overexpressed in Escherichia coli, and enzymology experiments demonstrated its unsaturated β-glucuronyl activity. Kinetic analysis of purified oligo-ulvans incubated with the new enzyme showed that the full substrate specificity is attained by three subsites that preferentially bind anionic residues (sulfated rhamnose, glucuronic/iduronic acid). The three-dimensional crystal structure of the native enzyme reveals that a trimeric organization is required for substrate binding and recognition at the +2 binding subsite. This novel unsaturated β-glucuronyl hydrolase is part of a previously uncharacterized subgroup of GH105 members and exhibits only a very limited sequence similarity to known unsaturated β-glucuronyl sequences previously found only in family GH88. Clan-O formed by families GH88 and GH105 was singular in the fact that it covered families acting on both axial and equatorial glycosidic linkages, respectively. The overall comparison of active site structures between enzymes from these two families highlights how that within family GH105, and unlike for classical glycoside hydrolysis, the hydrolysis of vinyl ether groups from unsaturated saccharides occurs independently of the α or β configuration of the cleaved linkage.
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Affiliation(s)
- Pi Nyvall Collén
- From the CNRS, Université Pierre et Marie Curie-Paris 6, Unité Mixte de Recherche 7139 "Marine Plants and Biomolecules," Station Biologique, F-29682 Roscoff Cedex, France
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49
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He Y, Roth C, Turkenburg JP, Davies GJ. Three-dimensional structure of a Streptomyces sviceus GNAT acetyltransferase with similarity to the C-terminal domain of the human GH84 O-GlcNAcase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:186-95. [PMID: 24419391 PMCID: PMC3919268 DOI: 10.1107/s1399004713029155] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 10/22/2013] [Indexed: 12/01/2022]
Abstract
The mammalian O-GlcNAc hydrolysing enzyme O-GlcNAcase (OGA) is a multi-domain protein with glycoside hydrolase activity in the N-terminus and with a C-terminal domain that has low sequence similarity to known acetyltransferases, prompting speculation, albeit controversial, that the C-terminal domain may function as a histone acetyltransferase (HAT). There are currently scarce data available regarding the structure and function of this C-terminal region. Here, a bacterial homologue of the human OGA C-terminal domain, an acetyltransferase protein (accession No. ZP_05014886) from Streptomyces sviceus (SsAT), was cloned and its crystal structure was solved to high resolution. The structure reveals a conserved protein core that has considerable structural homology to the acetyl-CoA (AcCoA) binding site of GCN5-related acetyltransferases (GNATs). Calorimetric data further confirm that SsAT is indeed able to bind AcCoA in solution with micromolar affinity. Detailed structural analysis provided insight into the binding of AcCoA. An acceptor-binding cavity was identified, indicating that the physiological substrate of SsAT may be a small molecule. Consistent with recently published work, the SsAT structure further questions a HAT function for the human OGA domain.
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Affiliation(s)
- Yuan He
- College of Chemistry and Materials Science, Northwest University, Xi’an 710069, People’s Republic of China
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Christian Roth
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Johan P. Turkenburg
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
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50
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Vitalis A, Caflisch A. Equilibrium Sampling Approach to the Interpretation of Electron Density Maps. Structure 2014; 22:156-67. [DOI: 10.1016/j.str.2013.10.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 10/22/2013] [Accepted: 10/26/2013] [Indexed: 10/25/2022]
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