401
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Structure and Dynamics of an Archeal Monoglyceride Lipase from Palaeococcus ferrophilus as Revealed by Crystallography and In Silico Analysis. Biomolecules 2021; 11:biom11040533. [PMID: 33916727 PMCID: PMC8065475 DOI: 10.3390/biom11040533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 01/06/2023] Open
Abstract
The crystallographic analysis of a lipase from Palaeococcus ferrophilus (PFL) previously annotated as a lysophospholipase revealed high structural conservation with other monoglyceride lipases, in particular in the lid domain and substrate binding pockets. In agreement with this observation, PFL was shown to be active on various monoacylglycerols. Molecular Dynamics (MD) studies performed in the absence and in the presence of ligands further allowed characterization of the dynamics of this system and led to a systematic closure of the lid compared to the crystal structure. However, the presence of ligands in the acyl-binding pocket stabilizes intermediate conformations compared to the crystal and totally closed structures. Several lid-stabilizing or closure elements were highlighted, i.e., hydrogen bonds between Ser117 and Ile204 or Asn142 and its facing amino acid lid residues, as well as Phe123. Thus, based on this complementary crystallographic and MD approach, we suggest that the crystal structure reported herein represents an open conformation, at least partially, of the PFL, which is likely stabilized by the ligand, and it brings to light several key structural features prone to participate in the closure of the lid.
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402
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Pérez-Moraga R, Forés-Martos J, Suay-García B, Duval JL, Falcó A, Climent J. A COVID-19 Drug Repurposing Strategy through Quantitative Homological Similarities Using a Topological Data Analysis-Based Framework. Pharmaceutics 2021; 13:pharmaceutics13040488. [PMID: 33918313 PMCID: PMC8066156 DOI: 10.3390/pharmaceutics13040488] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 02/06/2023] Open
Abstract
Since its emergence in March 2020, the SARS-CoV-2 global pandemic has produced more than 116 million cases and 2.5 million deaths worldwide. Despite the enormous efforts carried out by the scientific community, no effective treatments have been developed to date. We applied a novel computational pipeline aimed to accelerate the process of identifying drug repurposing candidates which allows us to compare three-dimensional protein structures. Its use in conjunction with two in silico validation strategies (molecular docking and transcriptomic analyses) allowed us to identify a set of potential drug repurposing candidates targeting three viral proteins (3CL viral protease, NSP15 endoribonuclease, and NSP12 RNA-dependent RNA polymerase), which included rutin, dexamethasone, and vemurafenib. This is the first time that a topological data analysis (TDA)-based strategy has been used to compare a massive number of protein structures with the final objective of performing drug repurposing to treat SARS-CoV-2 infection.
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Affiliation(s)
- Raul Pérez-Moraga
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain; (R.P.-M.); (J.F.-M.); (B.S.-G.)
- Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain
| | - Jaume Forés-Martos
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain; (R.P.-M.); (J.F.-M.); (B.S.-G.)
- Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain
- Biomedical Research Networking Center of Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Beatriz Suay-García
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain; (R.P.-M.); (J.F.-M.); (B.S.-G.)
- Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain
| | | | - Antonio Falcó
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain; (R.P.-M.); (J.F.-M.); (B.S.-G.)
- Departamento de Matemáticas, Física y Ciencias Tecnológicas, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain
- Correspondence: (A.F.); (J.C.)
| | - Joan Climent
- ESI International Chair@CEU-UCH, Universidad Cardenal Herrera-CEU, CEU Universities, San Bartolomé 55, Alfara del Patriarca, 46115 Valencia, Spain; (R.P.-M.); (J.F.-M.); (B.S.-G.)
- Departamento de Producción y Sanidad Animal, Salud Pública Veterinaria y Ciencia y Tecnología de los Alimentos, Universidad Cardenal Herrera-CEU, CEU Universities, C/Tirant lo Blanc 7, Alfara del Patriarca, 46115 Valencia, Spain
- Correspondence: (A.F.); (J.C.)
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403
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Zhou Z, Huang C, Zhou Z, Huang Z, Su L, Kang S, Chen X, Chen Q, He S, Rong X, Xiao F, Chen J, Chen S. Structural insight reveals SARS-CoV-2 ORF7a as an immunomodulating factor for human CD14 + monocytes. iScience 2021; 24:102187. [PMID: 33615195 PMCID: PMC7879101 DOI: 10.1016/j.isci.2021.102187] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 11/11/2020] [Accepted: 02/09/2021] [Indexed: 01/08/2023] Open
Abstract
Dysregulated immune cell responses have been linked to the severity of coronavirus disease 2019 (COVID-19), but the specific viral factors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were currently unknown. Herein, we reveal that the Immunoglobulin-like fold ectodomain of the viral protein SARS-CoV-2 ORF7a interacts with high efficiency to CD14+ monocytes in human peripheral blood, compared to pathogenic protein SARS-CoV ORF7a. The crystal structure of SARS-CoV-2 ORF7a at 2.2 Å resolution reveals three remarkable changes on the amphipathic side of the four-stranded β-sheet, implying a potential functional interface of the viral protein. Importantly, SARS-CoV-2 ORF7a coincubation with CD14+ monocytes ex vivo triggered a decrease in HLA-DR/DP/DQ expression levels and upregulated significant production of proinflammatory cytokines, including IL-6, IL-1β, IL-8, and TNF-α. Our work demonstrates that SARS-CoV-2 ORF7a is an immunomodulating factor for immune cell binding and triggers dramatic inflammatory responses, providing promising therapeutic drug targets for pandemic COVID-19.
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Affiliation(s)
- Ziliang Zhou
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Chunliu Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Zhechong Zhou
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Zhaoxia Huang
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Lili Su
- The Health Management Center, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Sisi Kang
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Xiaoxue Chen
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Qiuyue Chen
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Suhua He
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Xia Rong
- Institute of Clinical Transfusion, Guangzhou Blood Center, Guangzhou 510095, China
| | - Fei Xiao
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Jun Chen
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Key Laboratory of Tropical Disease Control of the Ministry of Education, Sun Yat-sen University, Guangzhou 510080, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Shoudeng Chen
- Molecular Imaging Center, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
- Department of Experimental Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
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404
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Zhu W, McQuarrie S, Grüschow S, McMahon SA, Graham S, Gloster TM, White MF. The CRISPR ancillary effector Can2 is a dual-specificity nuclease potentiating type III CRISPR defence. Nucleic Acids Res 2021; 49:2777-2789. [PMID: 33590098 PMCID: PMC7969007 DOI: 10.1093/nar/gkab073] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 12/26/2022] Open
Abstract
Cells and organisms have a wide range of mechanisms to defend against infection by viruses and other mobile genetic elements (MGE). Type III CRISPR systems detect foreign RNA and typically generate cyclic oligoadenylate (cOA) second messengers that bind to ancillary proteins with CARF (CRISPR associated Rossman fold) domains. This results in the activation of fused effector domains for antiviral defence. The best characterised CARF family effectors are the Csm6/Csx1 ribonucleases and DNA nickase Can1. Here we investigate a widely distributed CARF family effector with a nuclease domain, which we name Can2 (CRISPR ancillary nuclease 2). Can2 is activated by cyclic tetra-adenylate (cA4) and displays both DNase and RNase activity, providing effective immunity against plasmid transformation and bacteriophage infection in Escherichia coli. The structure of Can2 in complex with cA4 suggests a mechanism for the cA4-mediated activation of the enzyme, whereby an active site cleft is exposed on binding the activator. These findings extend our understanding of type III CRISPR cOA signalling and effector function.
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Affiliation(s)
- Wenlong Zhu
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Stuart McQuarrie
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Sabine Grüschow
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Stephen A McMahon
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Shirley Graham
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Tracey M Gloster
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
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405
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Klancher CA, Minasov G, Podicheti R, Rusch DB, Dalia TN, Satchell KJF, Neiditch MB, Dalia AB. The ChiS-Family DNA-Binding Domain Contains a Cryptic Helix-Turn-Helix Variant. mBio 2021; 12:e03287-20. [PMID: 33727356 PMCID: PMC8092284 DOI: 10.1128/mbio.03287-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/10/2021] [Indexed: 11/20/2022] Open
Abstract
Sequence-specific DNA-binding domains (DBDs) are conserved in all domains of life. These proteins carry out a variety of cellular functions, and there are a number of distinct structural domains already described that allow for sequence-specific DNA binding, including the ubiquitous helix-turn-helix (HTH) domain. In the facultative pathogen Vibrio cholerae, the chitin sensor ChiS is a transcriptional regulator that is critical for the survival of this organism in its marine reservoir. We recently showed that ChiS contains a cryptic DBD in its C terminus. This domain is not homologous to any known DBD, but it is a conserved domain present in other bacterial proteins. Here, we present the crystal structure of the ChiS DBD at a resolution of 1.28 Å. We find that the ChiS DBD contains an HTH domain that is structurally similar to those found in other DNA-binding proteins, like the LacI repressor. However, one striking difference observed in the ChiS DBD is that the canonical tight turn of the HTH is replaced with an insertion containing a β-sheet, a variant which we term the helix-sheet-helix. Through systematic mutagenesis of all positively charged residues within the ChiS DBD, we show that residues within and proximal to the ChiS helix-sheet-helix are critical for DNA binding. Finally, through phylogenetic analyses we show that the ChiS DBD is found in diverse proteobacterial proteins that exhibit distinct domain architectures. Together, these results suggest that the structure described here represents the prototypical member of the ChiS-family of DBDs.IMPORTANCE Regulating gene expression is essential in all domains of life. This process is commonly facilitated by the activity of DNA-binding transcription factors. There are diverse structural domains that allow proteins to bind to specific DNA sequences. The structural basis underlying how some proteins bind to DNA, however, remains unclear. Previously, we showed that in the major human pathogen Vibrio cholerae, the transcription factor ChiS directly regulates gene expression through a cryptic DNA-binding domain. This domain lacked homology to any known DNA-binding protein. In the current study, we determined the structure of the ChiS DNA-binding domain (DBD) and found that the ChiS-family DBD is a cryptic variant of the ubiquitous helix-turn-helix (HTH) domain. We further demonstrate that this domain is conserved in diverse proteins that may represent a novel group of transcriptional regulators.
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Affiliation(s)
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Ram Podicheti
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA
| | - Triana N Dalia
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Karla J F Satchell
- Center for Structural Genomics of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Matthew B Neiditch
- Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, New Jersey, USA
| | - Ankur B Dalia
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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406
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Schäfer L, Meinert-Berning C, Kobus S, Höppner A, Smits SHJ, Steinbüchel A. Crystal structure of the sugar acid-binding protein CxaP from a TRAP transporter in Advenella mimigardefordensis strain DPN7 T. FEBS J 2021; 288:4905-4917. [PMID: 33630388 DOI: 10.1111/febs.15789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/19/2021] [Accepted: 02/24/2021] [Indexed: 12/01/2022]
Abstract
Recently, CxaP, a sugar acid substrate binding protein (SBP) from Advenella mimigardefordensis strain DPN7T , was identified as part of a novel sugar uptake strategy. In the present study, the protein was successfully crystallized. Although several SBP structures of tripartite ATP-independent periplasmic transporters have already been solved, this is the first structure of an SBP accepting multiple sugar acid ligands. Protein crystals were obtained with bound d-xylonic acid, d-fuconic acid d-galactonic and d-gluconic acid, respectively. The protein shows the typical structure of an SBP of a tripartite ATP-independent periplasmic transporter consisting of two domains linked by a hinge and spanned by a long α-helix. By analysis of the structure, the substrate binding site of the protein was identified. The carboxylic group of the sugar acids interacts with Arg175, whereas the coordination of the hydroxylic groups at positions C2 and C3 is most probably realized by Arg154 and Asn151. Furthermore, it was observed that 2-keto-3-deoxy-d-gluconic acid is bound in protein crystals that were crystallized without the addition of any ligand, indicating that this molecule is prebound to the protein and is displaced by the other ligands if they are available. DATABASE: Structural data of CxaP complexes are available in the worldwide Protein Data Bank (https://www.rcsb.org) under the accession codes 7BBR (2-keto-3-deoxy-d-gluconic acid), 7BCR (d-galactonic acid), 7BCN (d-xylonic acid), 7BCO (d-fuconic acid) and 7BCP (d-gluconic acid).
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Affiliation(s)
- Lukas Schäfer
- Institute of Molecular Microbiology and Biotechnology, Westfälische Wilhelms University Münster, Münster, Germany
| | - Christina Meinert-Berning
- Institute of Molecular Microbiology and Biotechnology, Westfälische Wilhelms University Münster, Münster, Germany
| | - Stefanie Kobus
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Astrid Höppner
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sander H J Smits
- Center for Structural Studies, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexander Steinbüchel
- Institute of Molecular Microbiology and Biotechnology, Westfälische Wilhelms University Münster, Münster, Germany.,Environmental Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
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407
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Overview of structurally homologous flavoprotein oxidoreductases containing the low M r thioredoxin reductase-like fold - A functionally diverse group. Arch Biochem Biophys 2021; 702:108826. [PMID: 33684359 DOI: 10.1016/j.abb.2021.108826] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/23/2021] [Accepted: 02/27/2021] [Indexed: 01/12/2023]
Abstract
Structural studies show that enzymes have a limited number of unique folds, although structurally related enzymes have evolved to perform a large variety of functions. In this review, we have focused on enzymes containing the low molecular weight thioredoxin reductase (low Mr TrxR) fold. This fold consists of two domains, both containing a three-layer ββα sandwich Rossmann-like fold, serving as flavin adenine dinucleotide (FAD) and, in most cases, pyridine nucleotide (NAD(P)H) binding-domains. Based on a search of the Protein Data Bank for all published structures containing the low Mr TrxR-like fold, we here present a comprehensive overview of enzymes with this structural architecture. These range from TrxR-like ferredoxin/flavodoxin NAD(P)+ oxidoreductases, through glutathione reductase, to NADH peroxidase. Some enzymes are solely composed of the low Mr TrxR-like fold, while others contain one or two additional domains. In this review, we give a detailed description of selected enzymes containing only the low Mr TrxR-like fold, however, catalyzing a diversity of chemical reactions. Our overview of this structurally similar, yet functionally distinct group of flavoprotein oxidoreductases highlights the fascinating and increasing number of studies describing the diversity among these enzymes, especially during the last decade(s).
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408
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Yelland T, Le AH, Nikolaou S, Insall R, Machesky L, Ismail S. Structural Basis of CYRI-B Direct Competition with Scar/WAVE Complex for Rac1. Structure 2021; 29:226-237.e4. [PMID: 33217330 PMCID: PMC7955166 DOI: 10.1016/j.str.2020.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/07/2020] [Accepted: 11/02/2020] [Indexed: 01/16/2023]
Abstract
Rac1 is a major regulator of actin dynamics, with GTP-bound Rac1 promoting actin assembly via the Scar/WAVE complex. CYRI competes with Scar/WAVE for interaction with Rac1 in a feedback loop regulating actin dynamics. Here, we reveal the nature of the CYRI-Rac1 interaction, through crystal structures of CYRI-B lacking the N-terminal helix (CYRI-BΔN) and the CYRI-BΔN:Rac1Q61L complex, providing the molecular basis for CYRI-B regulation of the Scar/WAVE complex. We reveal CYRI-B as having two subdomains - an N-terminal Rac1 binding subdomain with a unique Rac1-effector interface and a C-terminal Ratchet subdomain that undergoes conformational changes induced by Rac1 binding. Finally, we show that the CYRI protein family, CYRI-A and CYRI-B can produce an autoinhibited hetero- or homodimers, adding an additional layer of regulation to Rac1 signaling.
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Affiliation(s)
| | | | | | - Robert Insall
- CRUK- Beatson Institute, Glasgow G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK
| | - Laura Machesky
- CRUK- Beatson Institute, Glasgow G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK.
| | - Shehab Ismail
- CRUK- Beatson Institute, Glasgow G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK; Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium.
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409
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Structure of a bacterial OapB protein with its OLE RNA target gives insights into the architecture of the OLE ribonucleoprotein complex. Proc Natl Acad Sci U S A 2021; 118:2020393118. [PMID: 33619097 PMCID: PMC7936274 DOI: 10.1073/pnas.2020393118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Bacterial noncoding RNAs (ncRNAs) play key roles in many biological processes including gene regulation, RNA processing and modification, and protein synthesis and translocation. OLE RNAs, found in many Gram-positive species, are one of the largest highly structured ncRNA classes whose biochemical functions remain unknown. In Bacillus halodurans, OLE RNAs interact with at least two proteins, OapA and OapB, which are required to assemble a functional OLE ribonucleoprotein (RNP) complex contributing to cellular responses to certain environmental stresses. We established X-ray structural models that reveal the sequence elements and tertiary structural features of OLE RNA that are critical for its specific recognition by OapB, which will aid future exploration of the biological and biochemical functions of the unusual OLE RNP complex. The OLE (ornate, large, and extremophilic) RNA class is one of the most complex and well-conserved bacterial noncoding RNAs known to exist. This RNA is known to be important for bacterial responses to stress caused by short-chain alcohols, cold, and elevated Mg2+ concentrations. These biological functions have been shown to require the formation of a ribonucleoprotein (RNP) complex including at least two protein partners: OLE-associated protein A (OapA) and OLE-associated protein B (OapB). OapB directly binds OLE RNA with high-affinity and specificity and is believed to assist in assembling the functional OLE RNP complex. To provide the atomic details of OapB–OLE RNA interaction and to potentially reveal previously uncharacterized protein–RNA interfaces, we determined the structure of OapB from Bacillus halodurans alone and in complex with an OLE RNA fragment at resolutions of 1.0 Å and 2.0 Å, respectively. The structure of OapB exhibits a K-shaped overall architecture wherein its conserved KOW motif and additional unique structural elements of OapB form a bipartite RNA-binding surface that docks to the P13 hairpin and P12.2 helix of OLE RNA. These high-resolution structures elucidate the molecular contacts used by OapB to form a stable RNP complex and explain the high conservation of sequences and structural features at the OapB–OLE RNA-binding interface. These findings provide insight into the role of OapB in the assembly and biological function of OLE RNP complex and can guide the exploration of additional possible OLE RNA-binding interactions present in OapB.
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410
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Kaur M, Sharma A, Kumar S, Singh G, Barnwal RP. SARS-CoV-2: Insights into its structural intricacies and functional aspects for drug and vaccine development. Int J Biol Macromol 2021; 179:45-60. [PMID: 33662418 PMCID: PMC7919520 DOI: 10.1016/j.ijbiomac.2021.02.212] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/04/2021] [Accepted: 02/27/2021] [Indexed: 12/11/2022]
Abstract
Globally, SARS-CoV-2 has emerged as threat to life and economy. Researchers are trying to find a cure against this pathogen but without much success. Several attempts have been made to understand the atomic level details of SARS-CoV-2 in the past few months. However, one review with all structural details for drug and vaccine development has been missing. Hence, this review aims to summarize key functional roles played by various domains of SARS-CoV-2 genome during its entry into the host, replication, repression of host immune response and overall viral life cycle. Additionally, various proteins of SARS-CoV-2 for finding a potent inhibitor have also been highlighted. To mitigate this deadly virus, an understanding of atomic level information, pathogenicity mechanisms and functions of different proteins in causing the infection is imperative. Thus, these structural details would finally pave the way for development of a potential drug/vaccine against the disease caused by SARS-CoV-2.
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Affiliation(s)
- Mandeep Kaur
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India; UIPS, Panjab University, Chandigarh 160014, India
| | - Santosh Kumar
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Gurpal Singh
- UIPS, Panjab University, Chandigarh 160014, India
| | - Ravi P Barnwal
- Department of Biophysics, Panjab University, Chandigarh 160014, India.
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411
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McLaughlin KJ. Developing a macromolecular crystallography driven CURE. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2021; 8:020406. [PMID: 33834085 PMCID: PMC8012065 DOI: 10.1063/4.0000089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
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412
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Ma R, Lian T, Huang R, Renn JP, Petersen JD, Zimmerberg J, Duffy PE, Tolia NH. Structural basis for placental malaria mediated by Plasmodium falciparum VAR2CSA. Nat Microbiol 2021; 6:380-391. [PMID: 33452495 PMCID: PMC7914210 DOI: 10.1038/s41564-020-00858-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/17/2020] [Indexed: 01/29/2023]
Abstract
Plasmodium falciparum VAR2CSA binds to chondroitin sulfate A (CSA) on the surface of the syncytiotrophoblast during placental malaria. This interaction facilitates placental sequestration of malaria parasites resulting in severe health outcomes for both the mother and her offspring. Furthermore, CSA is presented by diverse cancer cells and specific targeting of cells by VAR2CSA may become a viable approach for cancer treatment. In the present study, we determined the cryo-electron microscopy structures of the full-length ectodomain of VAR2CSA from P. falciparum strain NF54 in complex with CSA, and VAR2CSA from a second P. falciparum strain FCR3. The architecture of VAR2CSA is composed of a stable core flanked by a flexible arm. CSA traverses the core domain by binding within two channels and CSA binding does not induce major conformational changes in VAR2CSA. The CSA-binding elements are conserved across VAR2CSA variants and are flanked by polymorphic segments, suggesting immune selection outside the CSA-binding sites. This work provides paths for developing interventions against placental malaria and cancer.
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Affiliation(s)
- Rui Ma
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Tengfei Lian
- Laboratory of Membrane Proteins and Structural Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rick Huang
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan P. Renn
- Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer D. Petersen
- Section on Integrative Biophysics, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Joshua Zimmerberg
- Section on Integrative Biophysics, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Patrick E. Duffy
- Vaccine Development Unit, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA,Pathogenesis and Immunity Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Niraj H. Tolia
- Host-Pathogen Interactions and Structural Vaccinology Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA,Correspondence: (N.H.T.)
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413
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Cryo-EM structure of the Hippo signaling integrator human STRIPAK. Nat Struct Mol Biol 2021; 28:290-299. [PMID: 33633399 PMCID: PMC8315899 DOI: 10.1038/s41594-021-00564-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 01/20/2021] [Indexed: 01/31/2023]
Abstract
The striatin-interacting phosphatase and kinase (STRIPAK) complex is a large, multisubunit protein phosphatase 2A (PP2A) assembly that integrates diverse cellular signals in the Hippo pathway to regulate cell proliferation and survival. The architecture and assembly mechanism of this critical complex are poorly understood. Using cryo-EM, we determine the structure of the human STRIPAK core comprising PP2AA, PP2AC, STRN3, STRIP1, and MOB4 at 3.2-Å resolution. Unlike the canonical trimeric PP2A holoenzyme, STRIPAK contains four copies of STRN3 and one copy of each the PP2AA-C heterodimer, STRIP1, and MOB4. The STRN3 coiled-coil domains form an elongated homotetrameric scaffold that links the complex together. An inositol hexakisphosphate (IP6) is identified as a structural cofactor of STRIP1. Mutations of key residues at subunit interfaces disrupt the integrity of STRIPAK, causing aberrant Hippo pathway activation. Thus, STRIPAK is established as a noncanonical PP2A complex with four copies of regulatory STRN3 for enhanced signal integration.
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414
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Tumuluri VS, Rajgor V, Xu SY, Chouhan OP, Saikrishnan K. Mechanism of DNA cleavage by the endonuclease SauUSI: a major barrier to horizontal gene transfer and antibiotic resistance in Staphylococcus aureus. Nucleic Acids Res 2021; 49:2161-2178. [PMID: 33533920 PMCID: PMC7913695 DOI: 10.1093/nar/gkab042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 01/11/2021] [Accepted: 01/31/2021] [Indexed: 02/06/2023] Open
Abstract
Acquisition of foreign DNA by Staphylococcus aureus, including vancomycin resistance genes, is thwarted by the ATP-dependent endonuclease SauUSI. Deciphering the mechanism of action of SauUSI could unravel the reason how it singularly plays a major role in preventing horizontal gene transfer (HGT) in S. aureus. Here, we report a detailed biochemical and structural characterization of SauUSI, which reveals that in the presence of ATP, the enzyme can cleave DNA having a single or multiple target site/s. Remarkably, in the case of multiple target sites, the entire region of DNA flanked by two target sites is shred into smaller fragments by SauUSI. Crystal structure of SauUSI reveals a stable dimer held together by the nuclease domains, which are spatially arranged to hydrolyze the phosphodiester bonds of both strands of the duplex. Thus, the architecture of the dimeric SauUSI facilitates cleavage of either single-site or multi-site DNA. The structure also provides insights into the molecular basis of target recognition by SauUSI. We show that target recognition activates ATP hydrolysis by the helicase-like ATPase domain, which powers active directional movement (translocation) of SauUSI along the DNA. We propose that a pile-up of multiple translocating SauUSI molecules against a stationary SauUSI bound to a target site catalyzes random double-stranded breaks causing shredding of the DNA between two target sites. The extensive and irreparable damage of the foreign DNA by shredding makes SauUSI a potent barrier against HGT.
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Affiliation(s)
| | - Vrunda Rajgor
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Shuang-Yong Xu
- New England Biolabs Inc., Research Department, Ipswich, MA 01938, USA
| | - Om Prakash Chouhan
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Kayarat Saikrishnan
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
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415
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Wang B, Dong S, Li FL, Ma XQ. Structural basis for the exolytic activity of polysaccharide lyase family 6 alginate lyase BcAlyPL6 from human gut microbe Bacteroides clarus. Biochem Biophys Res Commun 2021; 547:111-117. [PMID: 33610038 DOI: 10.1016/j.bbrc.2021.02.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 01/08/2023]
Abstract
Alginate is the structural polysaccharide of the cell wall of brown algae, which is an important carbon source for marine life. The depolymerization of alginate is dependent on alginate lyases. Recent studies showed that the alginate utilization ability had been obtained by human gut microbes. In contrast to the great number of studies on alginate lyases from marine/soil organisms, studies on alginate lyases from gut microbes are still limited. Here, the structure of a polysaccharide lyase family 6 (PL6) alginate lyase from human gut microbe Bacteroides clarus was solved by X-ray crystallography, which represents the cluster of two-domain PL6 alginate lyases from Bacteroidetes. Similar with the two-domain alginate lyase AlyGC originated from marine bacterium, both the N terminal domain (NTD) and C terminal domain (CTD) of BcAlyPL6 show right-handed parallel β-helix fold. However, unlike AlyGC, which forms a homodimer, BcAlyPL6 functions as a monomer. Biochemical analysis indicates that the substrate binding affinity is mainly contributed by the NTD while the CTD of BcAlyPL6 is involved in the formation of -1 subsite, which is essential for substrate turnover rate. Furthermore, CTD is involved in shaping a closed catalytic pocket, and deletion of it leads to increased activity towards highly polymerized substrate. Structure comparison of PL6 family alginate lyases implies that the linkers of two-domain alginate lyases might have evolutionary relationship with the N/C terminal extension of single-domain lyases.
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Affiliation(s)
- Bing Wang
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
| | - Sheng Dong
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
| | - Fu-Li Li
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
| | - Xiao-Qing Ma
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China.
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416
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Zhang ZB, Xia YL, Dong GH, Fu YX, Liu SQ. Exploring the Cold-Adaptation Mechanism of Serine Hydroxymethyltransferase by Comparative Molecular Dynamics Simulations. Int J Mol Sci 2021; 22:1781. [PMID: 33670090 PMCID: PMC7916883 DOI: 10.3390/ijms22041781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Cold-adapted enzymes feature a lower thermostability and higher catalytic activity compared to their warm-active homologues, which are considered as a consequence of increased flexibility of their molecular structures. The complexity of the (thermo)stability-flexibility-activity relationship makes it difficult to define the strategies and formulate a general theory for enzyme cold adaptation. Here, the psychrophilic serine hydroxymethyltransferase (pSHMT) from Psychromonas ingrahamii and its mesophilic counterpart, mSHMT from Escherichia coli, were subjected to μs-scale multiple-replica molecular dynamics (MD) simulations to explore the cold-adaptation mechanism of the dimeric SHMT. The comparative analyses of MD trajectories reveal that pSHMT exhibits larger structural fluctuations and inter-monomer positional movements, a higher global flexibility, and considerably enhanced local flexibility involving the surface loops and active sites. The largest-amplitude motion mode of pSHMT describes the trends of inter-monomer dissociation and enlargement of the active-site cavity, whereas that of mSHMT characterizes the opposite trends. Based on the comparison of the calculated structural parameters and constructed free energy landscapes (FELs) between the two enzymes, we discuss in-depth the physicochemical principles underlying the stability-flexibility-activity relationships and conclude that (i) pSHMT adopts the global-flexibility mechanism to adapt to the cold environment and, (ii) optimizing the protein-solvent interactions and loosening the inter-monomer association are the main strategies for pSHMT to enhance its flexibility.
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Affiliation(s)
- Zhi-Bi Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (Z.-B.Z.); (Y.-L.X.); (G.-H.D.)
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine & Biomedical Engineering Research Center, Kunming Medical University, Kunming 650500, China
| | - Yuan-Ling Xia
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (Z.-B.Z.); (Y.-L.X.); (G.-H.D.)
| | - Guang-Heng Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (Z.-B.Z.); (Y.-L.X.); (G.-H.D.)
| | - Yun-Xin Fu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (Z.-B.Z.); (Y.-L.X.); (G.-H.D.)
- Human Genetics Center and Division of Biostatistics, School of Public Health, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Shu-Qun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (Z.-B.Z.); (Y.-L.X.); (G.-H.D.)
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417
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Macpherson A, Laabei M, Ahdash Z, Graewert MA, Birtley JR, Schulze MSE, Crennell S, Robinson SA, Holmes B, Oleinikovas V, Nilsson PH, Snowden J, Ellis V, Mollnes TE, Deane CM, Svergun D, Lawson AD, van den Elsen JM. The allosteric modulation of complement C5 by knob domain peptides. eLife 2021; 10:63586. [PMID: 33570492 PMCID: PMC7972453 DOI: 10.7554/elife.63586] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/11/2021] [Indexed: 12/22/2022] Open
Abstract
Bovines have evolved a subset of antibodies with ultra-long heavy chain complementarity determining regions that harbour cysteine-rich knob domains. To produce high-affinity peptides, we previously isolated autonomous 3–6 kDa knob domains from bovine antibodies. Here, we show that binding of four knob domain peptides elicits a range of effects on the clinically validated drug target complement C5. Allosteric mechanisms predominated, with one peptide selectively inhibiting C5 cleavage by the alternative pathway C5 convertase, revealing a targetable mechanistic difference between the classical and alternative pathway C5 convertases. Taking a hybrid biophysical approach, we present C5-knob domain co-crystal structures and, by solution methods, observed allosteric effects propagating >50 Å from the binding sites. This study expands the therapeutic scope of C5, presents new inhibitors, and introduces knob domains as new, low molecular weight antibody fragments, with therapeutic potential. Antibodies are proteins produced by the immune system that can selectively bind to other molecules and modify their behaviour. Cows are highly equipped at fighting-off disease-causing microbes due to the unique shape of some of their antibodies. Unlike other jawed vertebrates, cows’ antibodies contain an ultra-long loop region that contains a ‘knob domain’ which sticks out from the rest of the antibody. Recent research has shown that when detached, the knob domain behaves like an antibody fragment, and can independently bind to a range of different proteins. Antibody fragments are commonly developed in the laboratory to target proteins associated with certain diseases, such as arthritis and cancer. But it was unclear whether the knob domains from cows’ antibodies could also have therapeutic potential. To investigate this, Macpherson et al. studied how knob domains attach to complement C5, a protein in the inflammatory pathway which is a drug target for various diseases, including severe COVID-19. The experiments identified various knob domains that bind to complement C5 and inhibits its activity by altering its structure or movement. Further tests studying the structure of these interactions, led to the discovery of a common mechanism by which inhibitors can modify the behaviour of this inflammatory protein. Complement C5 is involved in numerous molecular pathways in the immune system, which means many of the drugs developed to inhibit its activity can also leave patients vulnerable to infection. However, one of the knob domains identified by Macpherson et al. was found to reduce the activity of complement C5 in some pathways, whilst leaving other pathways intact. This could potentially reduce the risk of bacterial infections which sometimes arise following treatment with these types of inhibitors. These findings highlight a new approach for developing drug inhibitors for complement C5. Furthermore, the ability of knob domains to bind to multiple sites of complement C5 suggests that this fragment could be used to target proteins associated with other diseases.
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Affiliation(s)
- Alex Macpherson
- UCB, Slough, United Kingdom.,Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Maisem Laabei
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | | | | | | | | | - Susan Crennell
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Sarah A Robinson
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | | | | | - Per H Nilsson
- UCB, Slough, United Kingdom.,Department of Chemistry and Biomedicine, Linnaeus University, Kalmar, Sweden.,Department of Immunology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | | | | | - Tom Eirik Mollnes
- Department of Immunology, Oslo University Hospital, University of Oslo, Oslo, Norway.,Research Laboratory, Bodø Hospital, K.G. Jebsen TREC, University of Tromsø, Tromsø, Norway.,Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Dmitri Svergun
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | | | - Jean Mh van den Elsen
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.,Centre for Therapeutic Innovation, University of Bath, Bath, United Kingdom
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418
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Abstract
Intracellular proliferation of Legionella pneumophila within a vacuole in human alveolar macrophages is essential for manifestation of Legionnaires’ pneumonia. Intravacuolar growth of the pathogen is totally dependent on remodeling the L. pneumophila-containing vacuole (LCV) by the ER and on its evasion of the endosomal-lysosomal degradation pathway. Diversion of the Legionella pneumophila-containing vacuole (LCV) from the host endosomal-lysosomal degradation pathway is one of the main virulence features essential for manifestation of Legionnaires’ pneumonia. Many of the ∼350 Dot/Icm-injected effectors identified in L. pneumophila have been shown to interfere with various host pathways and processes, but no L. pneumophila effector has ever been identified to be indispensable for lysosomal evasion. While most single effector mutants of L. pneumophila do not exhibit a defective phenotype within macrophages, we show that the MavE effector is essential for intracellular growth of L. pneumophila in human monocyte-derived macrophages (hMDMs) and amoebae and for intrapulmonary proliferation in mice. The mavE null mutant fails to remodel the LCV with endoplasmic reticulum (ER)-derived vesicles and is trafficked to the lysosomes where it is degraded, similar to formalin-killed bacteria. During infection of hMDMs, the MavE effector localizes to the poles of the LCV membrane. The crystal structure of MavE, resolved to 1.8 Å, reveals a C-terminal transmembrane helix, three copies of tyrosine-based sorting motifs, and an NPxY eukaryotic motif, which binds phosphotyrosine-binding domains present on signaling and adaptor eukaryotic proteins. Two point mutations within the NPxY motif result in attenuation of L. pneumophila in both hMDMs and amoeba. The substitution defects of P78 and D64 are associated with failure of vacuoles harboring the mutant to be remodeled by the ER and results in fusion of the vacuole to the lysosomes leading to bacterial degradation. Therefore, the MavE effector of L. pneumophila is indispensable for phagosome biogenesis and lysosomal evasion.
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419
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Andric V, Nevers A, Hazra D, Auxilien S, Menant A, Graille M, Palancade B, Rougemaille M. A scaffold lncRNA shapes the mitosis to meiosis switch. Nat Commun 2021; 12:770. [PMID: 33536434 PMCID: PMC7859202 DOI: 10.1038/s41467-021-21032-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/05/2021] [Indexed: 11/09/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) contribute to the regulation of gene expression in response to intra- or extracellular signals but the underlying molecular mechanisms remain largely unexplored. Here, we identify an uncharacterized lncRNA as a central player in shaping the meiotic gene expression program in fission yeast. We report that this regulatory RNA, termed mamRNA, scaffolds the antagonistic RNA-binding proteins Mmi1 and Mei2 to ensure their reciprocal inhibition and fine tune meiotic mRNA degradation during mitotic growth. Mechanistically, mamRNA allows Mmi1 to target Mei2 for ubiquitin-mediated downregulation, and conversely enables accumulating Mei2 to impede Mmi1 activity, thereby reinforcing the mitosis to meiosis switch. These regulations also occur within a unique Mmi1-containing nuclear body, positioning mamRNA as a spatially-confined sensor of Mei2 levels. Our results thus provide a mechanistic basis for the mutual control of gametogenesis effectors and further expand our vision of the regulatory potential of lncRNAs.
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Affiliation(s)
- Vedrana Andric
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Alicia Nevers
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- University Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Ditipriya Hazra
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France
- Department of Biochemistry, Oxford University, Oxford, OX1 3QU, UK
| | - Sylvie Auxilien
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Alexandra Menant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, France
| | - Benoit Palancade
- Université de Paris, CNRS, Institut Jacques Monod, F-75006, Paris, France
| | - Mathieu Rougemaille
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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420
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Kanao T, Hase N, Nakayama H, Yoshida K, Nishiura K, Kosaka M, Kamimura K, Hirano Y, Tamada T. Reaction mechanism of tetrathionate hydrolysis based on the crystal structure of tetrathionate hydrolase from Acidithiobacillus ferrooxidans. Protein Sci 2021; 30:328-338. [PMID: 33103311 PMCID: PMC7784748 DOI: 10.1002/pro.3984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 11/10/2022]
Abstract
Tetrathionate hydrolase (4THase) plays an important role in dissimilatory sulfur oxidation in the acidophilic iron- and sulfur-oxidizing bacterium Acidithiobacillus ferrooxidans. The structure of recombinant 4THase from A. ferrooxidans (Af-Tth) was determined by X-ray crystallography to a resolution of 1.95 Å. Af-Tth is a homodimer, and its monomer structure exhibits an eight-bladed β-propeller motif. Two insertion loops participate in dimerization, and one loop forms a cavity with the β-propeller region. We observed unexplained electron densities in this cavity of the substrate-soaked structure. The anomalous difference map generated using diffraction data collected at a wavelength of 1.9 Å indicated the presence of polymerized sulfur atoms. Asp325, a highly conserved residue among 4THases, was located near the polymerized sulfur atoms. 4THase activity was completely abolished in the site-specific Af-Tth D325N variant, suggesting that Asp325 plays a crucial role in the first step of tetrathionate hydrolysis. Considering that the Af-Tth reaction occurs only under acidic pH, Asp325 acts as an acid for the tetrathionate hydrolysis reaction. The polymerized sulfur atoms in the active site cavity may represent the intermediate product in the subsequent step.
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Affiliation(s)
- Tadayoshi Kanao
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Naruki Hase
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Hisayuki Nakayama
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Kyoya Yoshida
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Kazumi Nishiura
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Megumi Kosaka
- Department of Instrumental Analysis, Advanced Science Research CenterOkayama UniversityOkayamaJapan
| | - Kazuo Kamimura
- Department of Biofunctional Chemistry, Division of Agricultural and Life Science, Graduate School of Environmental and Life ScienceOkayama UniversityOkayamaJapan
| | - Yu Hirano
- Institute for Quantum Life ScienceNational Institutes for Quantum and Radiological Science and TechnologyTokaiJapan
| | - Taro Tamada
- Institute for Quantum Life ScienceNational Institutes for Quantum and Radiological Science and TechnologyTokaiJapan
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421
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Weber JJ, Kashipathy MM, Battaile KP, Go E, Desaire H, Kanost MR, Lovell S, Gorman MJ. Structural insight into the novel iron-coordination and domain interactions of transferrin-1 from a model insect, Manduca sexta. Protein Sci 2021; 30:408-422. [PMID: 33197096 PMCID: PMC7784759 DOI: 10.1002/pro.3999] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 11/07/2022]
Abstract
Transferrins function in iron sequestration and iron transport by binding iron tightly and reversibly. Vertebrate transferrins coordinate iron through interactions with two tyrosines, an aspartate, a histidine, and a carbonate anion, and conformational changes that occur upon iron binding and release have been described. Much less is known about the structure and functions of insect transferrin-1 (Tsf1), which is present in hemolymph and influences iron homeostasis mostly by unknown mechanisms. Amino acid sequence and biochemical analyses have suggested that iron coordination by Tsf1 differs from that of the vertebrate transferrins. Here we report the first crystal structure (2.05 Å resolution) of an insect transferrin. Manduca sexta (MsTsf1) in the holo form exhibits a bilobal fold similar to that of vertebrate transferrins, but its carboxyl-lobe adopts a novel orientation and contacts with the amino-lobe. The structure revealed coordination of a single Fe3+ ion in the amino-lobe through Tyr90, Tyr204, and two carbonate anions. One carbonate anion is buried near the ferric ion and is coordinated by four residues, whereas the other carbonate anion is solvent exposed and coordinated by Asn121. Notably, these residues are highly conserved in Tsf1 orthologs. Docking analysis suggested that the solvent exposed carbonate position is capable of binding alternative anions. These findings provide a structural basis for understanding Tsf1 function in iron sequestration and transport in insects as well as insight into the similarities and differences in iron homeostasis between insects and humans.
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Affiliation(s)
- Jacob J. Weber
- Department of Biochemistry and Molecular BiophysicsKansas State UniversityManhattanKansasUSA
| | - Maithri M. Kashipathy
- Protein Structure Laboratory, Del Shankel Structural Biology CenterUniversity of KansasLawrenceKansasUSA
| | | | - Eden Go
- Department of ChemistryUniversity of KansasLawrenceKansasUSA
| | - Heather Desaire
- Department of ChemistryUniversity of KansasLawrenceKansasUSA
| | - Michael R. Kanost
- Department of Biochemistry and Molecular BiophysicsKansas State UniversityManhattanKansasUSA
| | - Scott Lovell
- Protein Structure Laboratory, Del Shankel Structural Biology CenterUniversity of KansasLawrenceKansasUSA
| | - Maureen J. Gorman
- Department of Biochemistry and Molecular BiophysicsKansas State UniversityManhattanKansasUSA
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422
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Jessop M, Felix J, Gutsche I. AAA+ ATPases: structural insertions under the magnifying glass. Curr Opin Struct Biol 2021; 66:119-128. [PMID: 33246198 PMCID: PMC7973254 DOI: 10.1016/j.sbi.2020.10.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/19/2020] [Accepted: 10/27/2020] [Indexed: 11/29/2022]
Abstract
AAA+ ATPases are a diverse protein superfamily which power a vast number of cellular processes, from protein degradation to genome replication and ribosome biogenesis. The latest advances in cryo-EM have resulted in a spectacular increase in the number and quality of AAA+ ATPase structures. This abundance of new information enables closer examination of different types of structural insertions into the conserved core, revealing discrepancies in the current classification of AAA+ modules into clades. Additionally, combined with biochemical data, it has allowed rapid progress in our understanding of structure-functional relationships and provided arguments both in favour and against the existence of a unifying molecular mechanism for the ATPase activity and action on substrates, stimulating further intensive research.
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Affiliation(s)
- Matthew Jessop
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044 Grenoble, France.
| | - Jan Felix
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044 Grenoble, France
| | - Irina Gutsche
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des martyrs, F-38044 Grenoble, France.
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423
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Perez-Garcia P, Kobus S, Gertzen CGW, Hoeppner A, Holzscheck N, Strunk CH, Huber H, Jaeger KE, Gohlke H, Kovacic F, Smits SHJ, Streit WR, Chow J. A promiscuous ancestral enzyme´s structure unveils protein variable regions of the highly diverse metallo-β-lactamase family. Commun Biol 2021; 4:132. [PMID: 33514861 PMCID: PMC7846560 DOI: 10.1038/s42003-021-01671-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 01/06/2021] [Indexed: 01/30/2023] Open
Abstract
The metallo-β-lactamase fold is an ancient protein structure present in numerous enzyme families responsible for diverse biological processes. The crystal structure of the hyperthermostable crenarchaeal enzyme Igni18 from Ignicoccus hospitalis was solved at 2.3 Å and could resemble a possible first archetype of a multifunctional metallo-β-lactamase. Ancestral enzymes at the evolutionary origin are believed to be promiscuous all-rounders. Consistently, Igni18´s activity can be cofactor-dependently directed from β-lactamase to lactonase, lipase, phosphodiesterase, phosphotriesterase or phospholipase. Its core-domain is highly conserved within metallo-β-lactamases from Bacteria, Archaea and Eukarya and gives insights into evolution and function of enzymes from this superfamily. Structural alignments with diverse metallo-β-lactamase-fold-containing enzymes allowed the identification of Protein Variable Regions accounting for modulation of activity, specificity and oligomerization patterns. Docking of different substrates within the active sites revealed the basis for the crucial cofactor dependency of this enzyme superfamily.
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Affiliation(s)
- Pablo Perez-Garcia
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany
| | - Stefanie Kobus
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Christoph G W Gertzen
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Astrid Hoeppner
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Nicholas Holzscheck
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany
| | - Christoph Heinrich Strunk
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, 52426, Jülich, Germany
| | - Harald Huber
- Institute for Microbiology and Archaeal Center, Regensburg University, 93035, Regensburg, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, 52426, Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) & Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf, 52426, Jülich, Germany
| | - Sander H J Smits
- Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Wolfgang R Streit
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany
| | - Jennifer Chow
- Department of Microbiology and Biotechnology, University of Hamburg, Ohnhorststrasse 18, 22609, Hamburg, Germany.
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424
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Gabel C, Li Z, Zhang H, Chang L. Structural basis for inhibition of the type I-F CRISPR-Cas surveillance complex by AcrIF4, AcrIF7 and AcrIF14. Nucleic Acids Res 2021; 49:584-594. [PMID: 33332569 PMCID: PMC7797054 DOI: 10.1093/nar/gkaa1199] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/22/2020] [Accepted: 12/14/2020] [Indexed: 12/21/2022] Open
Abstract
CRISPR-Cas systems are adaptive immune systems in bacteria and archaea to defend against mobile genetic elements (MGEs) and have been repurposed as genome editing tools. Anti-CRISPR (Acr) proteins are produced by MGEs to counteract CRISPR-Cas systems and can be used to regulate genome editing by CRISPR techniques. Here, we report the cryo-EM structures of three type I-F Acr proteins, AcrIF4, AcrIF7 and AcrIF14, bound to the type I-F CRISPR-Cas surveillance complex (the Csy complex) from Pseudomonas aeruginosa. AcrIF4 binds to an unprecedented site on the C-terminal helical bundle of Cas8f subunit, precluding conformational changes required for activation of the Csy complex. AcrIF7 mimics the PAM duplex of target DNA and is bound to the N-terminal DNA vise of Cas8f. Two copies of AcrIF14 bind to the thumb domains of Cas7.4f and Cas7.6f, preventing hybridization between target DNA and the crRNA. Our results reveal structural detail of three AcrIF proteins, each binding to a different site on the Csy complex for inhibiting degradation of MGEs.
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Affiliation(s)
- Clinton Gabel
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Zhuang Li
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Heng Zhang
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Leifu Chang
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA.,Purdue University Center for Cancer Research, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
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425
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Choi WS, Liu B, Shen Z, Yang W. Structure of human BCCIP and implications for binding and modification of partner proteins. Protein Sci 2021; 30:693-699. [PMID: 33452718 DOI: 10.1002/pro.4026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/10/2021] [Accepted: 01/12/2021] [Indexed: 11/09/2022]
Abstract
BCCIP was isolated based on its interactions with tumor suppressors BRCA2 and p21. Knockdown or knockout of BCCIP causes embryonic lethality in mice. BCCIP deficient cells exhibit impaired cell proliferation and chromosome instability. BCCIP also plays a key role in biogenesis of ribosome 60S subunits. BCCIP is conserved from yeast to humans, but it has no discernible sequence similarity to proteins of known structures. Here we report two crystal structures of an N-terminal truncated human BCCIPβ, consisting of residues 61-314. Structurally BCCIP is similar to GCN5-related acetyltransferases (GNATs) but contains different sequence motifs. Moreover, both acetyl-CoA and substrate-binding grooves are altered in BCCIP. A large 19-residue flap over the putative CoA binding site adopts either an open or closed conformation in BCCIP. The substrate binding groove is significantly reduced in size and is positively charged despite the acidic isoelectric point of BCCIP. BCCIP has potential binding sites for partner proteins and may have enzymatic activity.
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Affiliation(s)
- Woo Suk Choi
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, USA
| | - Bochao Liu
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Zhiyuan Shen
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Wei Yang
- Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, USA
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426
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Gamiz-Arco G, Gutierrez-Rus LI, Risso VA, Ibarra-Molero B, Hoshino Y, Petrović D, Justicia J, Cuerva JM, Romero-Rivera A, Seelig B, Gavira JA, Kamerlin SCL, Gaucher EA, Sanchez-Ruiz JM. Heme-binding enables allosteric modulation in an ancient TIM-barrel glycosidase. Nat Commun 2021; 12:380. [PMID: 33452262 PMCID: PMC7810902 DOI: 10.1038/s41467-020-20630-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 12/11/2020] [Indexed: 12/11/2022] Open
Abstract
Glycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ∼5500 reported crystallographic structures of ∼1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme tightly and stoichiometrically at a well-defined buried site. Heme binding rigidifies this TIM-barrel and allosterically enhances catalysis. Our work demonstrates the capability of ancestral protein reconstructions to reveal valuable but unexpected biomolecular features when sampling distant sequence space. The potential of the ancestral glycosidase as a scaffold for custom catalysis and biosensor engineering is discussed. Family 1 glycosidases (GH1) are present in the three domains of life and share classical TIM-barrel fold. Structural and biochemical analyses of a resurrected ancestral GH1 enzyme reveal heme binding, not known in its modern descendants. Heme rigidifies the TIM-barrel and allosterically enhances catalysis.
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Affiliation(s)
- Gloria Gamiz-Arco
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Luis I Gutierrez-Rus
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Valeria A Risso
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Beatriz Ibarra-Molero
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Yosuke Hoshino
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Dušan Petrović
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23, Uppsala, Sweden.,Hit Discovery, Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, 431 50, Gothenburg, Sweden
| | - Jose Justicia
- Departamento de Quimica Organica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Juan Manuel Cuerva
- Departamento de Quimica Organica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain
| | - Adrian Romero-Rivera
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23, Uppsala, Sweden
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America, & BioTechnology Institute, University of Minnesota, St. Paul, MN, USA
| | - Jose A Gavira
- Laboratorio de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, Avenida de las Palmeras 4, Granada, 18100, Armilla, Spain
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Chemistry-BMC, Uppsala University, BMC Box 576, S-751 23, Uppsala, Sweden.
| | - Eric A Gaucher
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA.
| | - Jose M Sanchez-Ruiz
- Departamento de Quimica Fisica. Facultad de Ciencias, Unidad de Excelencia de Quimica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071, Granada, Spain.
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427
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Sowa ST, Moilanen A, Biterova E, Saaranen MJ, Lehtiö L, Ruddock LW. High-resolution Crystal Structure of Human pERp1, A Saposin-like Protein Involved in IgA, IgM and Integrin Maturation in the Endoplasmic Reticulum. J Mol Biol 2021; 433:166826. [PMID: 33453188 DOI: 10.1016/j.jmb.2021.166826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/05/2021] [Accepted: 01/05/2021] [Indexed: 01/24/2023]
Abstract
The folding of disulfide bond containing proteins in the endoplasmic reticulum (ER) is a complex process that requires protein folding factors, some of which are protein-specific. The ER resident saposin-like protein pERp1 (MZB1, CNPY5) is crucial for the correct folding of IgA, IgM and integrins. pERp1 also plays a role in ER calcium homeostasis and plasma cell mobility. As an important factor for proper IgM maturation and hence immune function, pERp1 is upregulated in many auto-immune diseases. This makes it a potential therapeutic target. pERp1 belongs to the CNPY family of ER resident saposin-like proteins. To date, five of these proteins have been identified. All are implicated in protein folding and all contain a saposin-like domain. All previously structurally characterized saposins are involved in lipid binding. However, there are no reports of CNPY family members interacting with lipids, suggesting a novel function for the saposin fold. However, the molecular mechanisms of their function remain elusive. To date, no structure of any CNPY protein has been reported. Here, we present the high-resolution (1.4 Å) crystal structure of human pERp1 and confirm that it has a saposin-fold with unique structural elements not present in other saposin-fold structures. The implications for the role of CNPY proteins in protein folding in the ER are discussed.
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Affiliation(s)
- Sven T Sowa
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland; Biocenter Oulu, Aapistie 5, 90220 Oulu, Finland.
| | - Antti Moilanen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland.
| | - Ekaterina Biterova
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland
| | - Mirva J Saaranen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland.
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland; Biocenter Oulu, Aapistie 5, 90220 Oulu, Finland.
| | - Lloyd W Ruddock
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7, 90220 Oulu, Finland.
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428
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Mestre MR, González-Delgado A, Gutiérrez-Rus LI, Martínez-Abarca F, Toro N. Systematic prediction of genes functionally associated with bacterial retrons and classification of the encoded tripartite systems. Nucleic Acids Res 2021; 48:12632-12647. [PMID: 33275130 PMCID: PMC7736814 DOI: 10.1093/nar/gkaa1149] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/05/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial retrons consist of a reverse transcriptase (RT) and a contiguous non-coding RNA (ncRNA) gene. One third of annotated retrons carry additional open reading frames (ORFs), the contribution and significance of which in retron biology remains to be determined. In this study we developed a computational pipeline for the systematic prediction of genes specifically associated with retron RTs based on a previously reported large dataset representative of the diversity of prokaryotic RTs. We found that retrons generally comprise a tripartite system composed of the ncRNA, the RT and an additional protein or RT-fused domain with diverse enzymatic functions. These retron systems are highly modular, and their components have coevolved to different extents. Based on the additional module, we classified retrons into 13 types, some of which include additional variants. Our findings provide a basis for future studies on the biological function of retrons and for expanding their biotechnological applications.
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Affiliation(s)
- Mario Rodríguez Mestre
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Alejandro González-Delgado
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Luis I Gutiérrez-Rus
- Departamento de Química Física. Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Francisco Martínez-Abarca
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
| | - Nicolás Toro
- Structure, Dynamics and Function of Rhizobacterial Genomes, Grupo de Ecología Genética de la Rizosfera, Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/ Profesor Albareda 1, 18008 Granada, Spain
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429
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Shen M, Dhingra N, Wang Q, Cheng C, Zhu S, Tian X, Yu J, Gong X, Li X, Zhang H, Xu X, Zhai L, Xie M, Gao Y, Deng H, He Y, Niu H, Zhao X, Xiang S. Structural basis for the multi-activity factor Rad5 in replication stress tolerance. Nat Commun 2021; 12:321. [PMID: 33436623 PMCID: PMC7804152 DOI: 10.1038/s41467-020-20538-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
The yeast protein Rad5 and its orthologs in other eukaryotes promote replication stress tolerance and cell survival using their multiple activities, including ubiquitin ligase, replication fork remodeling and DNA lesion targeting activities. Here, we present the crystal structure of a nearly full-length Rad5 protein. The structure shows three distinct, but well-connected, domains required for Rad5’s activities. The spatial arrangement of these domains suggest that different domains can have autonomous activities but also undergo intrinsic coordination. Moreover, our structural, biochemical and cellular studies demonstrate that Rad5’s HIRAN domain mediates interactions with the DNA metabolism maestro factor PCNA and contributes to its poly-ubiquitination, binds to DNA and contributes to the Rad5-catalyzed replication fork regression, defining a new type of HIRAN domains with multiple activities. Our work provides a framework to understand how Rad5 integrates its various activities in replication stress tolerance. Rad5 is a hub connecting three replication stress tolerance pathways. Here, the authors present the 3.3 Å crystal structure of a N-terminal truncated K.lactis Rad5 construct that reveals the spatial arrangement of the HIRAN, Snf2 and RING domains and structure-guided in vitro and in vivo experiments reveal multiple activities of the yeast Rad5 HIRAN domain among them a role in binding PCNA and supporting its ubiquitination.
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Affiliation(s)
- Miaomiao Shen
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, P. R. China.,Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, 300070, Tianjin, P. R. China.,The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Tianjin Medical University, 300070, Tianjin, P. R. China
| | - Nalini Dhingra
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Quan Wang
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, Bloomington, IN, 47405, USA
| | - Chen Cheng
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 201210, Shanghai, P. R. China
| | - Songbiao Zhu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, P. R. China
| | - Xiaolin Tian
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, P. R. China
| | - Jun Yu
- CAS Key Laboratory of Nutrition, Metabolism and Food safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, P. R. China
| | - Xiaoxin Gong
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, P. R. China.,Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, 300070, Tianjin, P. R. China.,The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Tianjin Medical University, 300070, Tianjin, P. R. China
| | - Xuzhichao Li
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, P. R. China.,Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, 300070, Tianjin, P. R. China.,The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Tianjin Medical University, 300070, Tianjin, P. R. China
| | - Hongwei Zhang
- CAS Key Laboratory of Nutrition, Metabolism and Food safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, P. R. China
| | - Xin Xu
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, P. R. China.,Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, 300070, Tianjin, P. R. China.,The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Tianjin Medical University, 300070, Tianjin, P. R. China
| | - Liting Zhai
- CAS Key Laboratory of Nutrition, Metabolism and Food safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, P. R. China
| | - Min Xie
- CAS Key Laboratory of Nutrition, Metabolism and Food safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, P. R. China
| | - Ying Gao
- CAS Key Laboratory of Nutrition, Metabolism and Food safety, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200031, Shanghai, P. R. China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, 100084, Beijing, P. R. China
| | - Yongning He
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, 201210, Shanghai, P. R. China
| | - Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University Bloomington, Bloomington, IN, 47405, USA
| | - Xiaolan Zhao
- Molecular Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Song Xiang
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 300070, Tianjin, P. R. China. .,Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Medical University, 300070, Tianjin, P. R. China. .,The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Tianjin Medical University, 300070, Tianjin, P. R. China.
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430
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Nygaard R, Yu J, Kim J, Ross DR, Parisi G, Clarke OB, Virshup DM, Mancia F. Structural Basis of WLS/Evi-Mediated Wnt Transport and Secretion. Cell 2021; 184:194-206.e14. [PMID: 33357447 PMCID: PMC7797000 DOI: 10.1016/j.cell.2020.11.038] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/26/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022]
Abstract
Wnts are evolutionarily conserved ligands that signal at short range to regulate morphogenesis, cell fate, and stem cell renewal. The first and essential steps in Wnt secretion are their O-palmitoleation and subsequent loading onto the dedicated transporter Wntless/evenness interrupted (WLS/Evi). We report the 3.2 Å resolution cryogenic electron microscopy (cryo-EM) structure of palmitoleated human WNT8A in complex with WLS. This is accompanied by biochemical experiments to probe the physiological implications of the observed association. The WLS membrane domain has close structural homology to G protein-coupled receptors (GPCRs). A Wnt hairpin inserts into a conserved hydrophobic cavity in the GPCR-like domain, and the palmitoleate protrudes between two helices into the bilayer. A conformational switch of highly conserved residues on a separate Wnt hairpin might contribute to its transfer to receiving cells. This work provides molecular-level insights into a central mechanism in animal body plan development and stem cell biology.
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Affiliation(s)
- Rie Nygaard
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Jia Yu
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Jonathan Kim
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Daniel R Ross
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Giacomo Parisi
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - David M Virshup
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; Department of Pediatrics, Duke University School of Medicine, Durham, NC 27705, USA.
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA.
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431
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Zhou J, Pecqueur L, Aučynaitė A, Fuchs J, Rutkienė R, Vaitekūnas J, Meškys R, Boll M, Fontecave M, Urbonavičius J, Golinelli‐Pimpaneau B. Structural Evidence for a [4Fe‐5S] Intermediate in the Non‐Redox Desulfuration of Thiouracil. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202011211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jingjing Zhou
- Laboratoire de Chimie des Processus Biologiques UMR 8229 CNRS Collège de France Sorbonne Université Paris CEDEX 05 France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques UMR 8229 CNRS Collège de France Sorbonne Université Paris CEDEX 05 France
| | - Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology Institute of Biochemistry Life Sciences Center Vilnius University Vilnius Lithuania
| | - Jonathan Fuchs
- Faculty of Biology—Microbiology University of Freiburg 79104 Freiburg Germany
| | - Rasa Rutkienė
- Department of Molecular Microbiology and Biotechnology Institute of Biochemistry Life Sciences Center Vilnius University Vilnius Lithuania
| | - Justas Vaitekūnas
- Department of Molecular Microbiology and Biotechnology Institute of Biochemistry Life Sciences Center Vilnius University Vilnius Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology Institute of Biochemistry Life Sciences Center Vilnius University Vilnius Lithuania
| | - Matthias Boll
- Faculty of Biology—Microbiology University of Freiburg 79104 Freiburg Germany
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques UMR 8229 CNRS Collège de France Sorbonne Université Paris CEDEX 05 France
| | - Jaunius Urbonavičius
- Department of Molecular Microbiology and Biotechnology Institute of Biochemistry Life Sciences Center Vilnius University Vilnius Lithuania
- Department of Chemistry and Bioengineering Vilnius Gediminas Technical University Vilnius Lithuania
| | - Béatrice Golinelli‐Pimpaneau
- Laboratoire de Chimie des Processus Biologiques UMR 8229 CNRS Collège de France Sorbonne Université Paris CEDEX 05 France
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432
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Tamura K, Dejean G, Van Petegem F, Brumer H. Distinct protein architectures mediate species-specific beta-glucan binding and metabolism in the human gut microbiota. J Biol Chem 2021; 296:100415. [PMID: 33587952 PMCID: PMC7974029 DOI: 10.1016/j.jbc.2021.100415] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/02/2021] [Accepted: 02/10/2021] [Indexed: 12/12/2022] Open
Abstract
Complex glycans that evade our digestive system are major nutrients that feed the human gut microbiota (HGM). The prevalence of Bacteroidetes in the HGM of populations worldwide is engendered by the evolution of polysaccharide utilization loci (PULs), which encode concerted protein systems to utilize the myriad complex glycans in our diets. Despite their crucial roles in glycan recognition and transport, cell-surface glycan-binding proteins (SGBPs) remained understudied cogs in the PUL machinery. Here, we report the structural and biochemical characterization of a suite of SGBP-A and SGBP-B structures from three syntenic β(1,3)-glucan utilization loci (1,3GULs) from Bacteroides thetaiotaomicron (Bt), Bacteroides uniformis (Bu), and B. fluxus (Bf), which have varying specificities for distinct β-glucans. Ligand complexes provide definitive insight into β(1,3)-glucan selectivity in the HGM, including structural features enabling dual β(1,3)-glucan/mixed-linkage β(1,3)/β(1,4)-glucan-binding capability in some orthologs. The tertiary structural conservation of SusD-like SGBPs-A is juxtaposed with the diverse architectures and binding modes of the SGBPs-B. Specifically, the structures of the trimodular BtSGBP-B and BuSGBP-B revealed a tandem repeat of carbohydrate-binding module-like domains connected by long linkers. In contrast, BfSGBP-B comprises a bimodular architecture with a distinct β-barrel domain at the C terminus that bears a shallow binding canyon. The molecular insights obtained here contribute to our fundamental understanding of HGM function, which in turn may inform tailored microbial intervention therapies.
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Affiliation(s)
- Kazune Tamura
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, The Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guillaume Dejean
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, The Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, The Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
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433
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The evolutionary relationship of S15/NS1RNA binding domains with a similar protein domain pattern - A computational approach. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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434
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Cisneros-Martínez AM, Becerra A, Lazcano A. Ancient gene duplications in RNA viruses revealed by protein tertiary structure comparisons. Virus Evol 2021; 7:veab019. [PMID: 33758672 PMCID: PMC7967035 DOI: 10.1093/ve/veab019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
To date only a handful of duplicated genes have been described in RNA viruses. This shortage can be attributed to different factors, including the RNA viruses with high mutation rate that would make a large genome more prone to acquire deleterious mutations. This may explain why sequence-based approaches have only found duplications in their most recent evolutionary history. To detect earlier duplications, we performed protein tertiary structure comparisons for every RNA virus family represented in the Protein Data Bank. We present a list of thirty pairs of possible paralogs with <30 per cent sequence identity. It is argued that these pairs are the outcome of six duplication events. These include the α and β subunits of the fungal toxin KP6 present in the dsRNA Ustilago maydis virus (family Totiviridae), the SARS-CoV (Coronaviridae) nsp3 domains SUD-N, SUD-M and X-domain, the Picornavirales (families Picornaviridae, Dicistroviridae, Iflaviridae and Secoviridae) capsid proteins VP1, VP2 and VP3, and the Enterovirus (family Picornaviridae) 3C and 2A cysteine-proteases. Protein tertiary structure comparisons may reveal more duplication events as more three-dimensional protein structures are determined and suggests that, although still rare, gene duplications may be more frequent in RNA viruses than previously thought. Keywords: gene duplications; RNA viruses.
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Affiliation(s)
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Antonio Lazcano
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- El Colegio Nacional, Donceles 104, Centro Histórico, Mexico City, Mexico
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435
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Slavik KM, Morehouse BR, Ragucci AE, Zhou W, Ai X, Chen Y, Li L, Wei Z, Bähre H, König M, Seifert R, Lee ASY, Cai H, Imler JL, Kranzusch PJ. cGAS-like receptors sense RNA and control 3'2'-cGAMP signalling in Drosophila. Nature 2021; 597:109-113. [PMID: 34261127 PMCID: PMC8410604 DOI: 10.1038/s41586-021-03743-5] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/21/2021] [Indexed: 02/07/2023]
Abstract
Cyclic GMP-AMP synthase (cGAS) is a cytosolic DNA sensor that produces the second messenger cG[2'-5']pA[3'-5']p (2'3'-cGAMP) and controls activation of innate immunity in mammalian cells1-5. Animal genomes typically encode multiple proteins with predicted homology to cGAS6-10, but the function of these uncharacterized enzymes is unknown. Here we show that cGAS-like receptors (cGLRs) are innate immune sensors that are capable of recognizing divergent molecular patterns and catalysing synthesis of distinct nucleotide second messenger signals. Crystal structures of human and insect cGLRs reveal a nucleotidyltransferase signalling core shared with cGAS and a diversified primary ligand-binding surface modified with notable insertions and deletions. We demonstrate that surface remodelling of cGLRs enables altered ligand specificity and used a forward biochemical screen to identify cGLR1 as a double-stranded RNA sensor in the model organism Drosophila melanogaster. We show that RNA recognition activates Drosophila cGLR1 to synthesize the novel product cG[3'-5']pA[2'-5']p (3'2'-cGAMP). A crystal structure of Drosophila stimulator of interferon genes (dSTING) in complex with 3'2'-cGAMP explains selective isomer recognition, and 3'2'-cGAMP induces an enhanced antiviral state in vivo that protects from viral infection. Similar to radiation of Toll-like receptors in pathogen immunity, our results establish cGLRs as a diverse family of metazoan pattern recognition receptors.
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Affiliation(s)
- Kailey M. Slavik
- grid.38142.3c000000041936754XDepartment of Microbiology, Harvard Medical School, Boston, MA USA ,grid.65499.370000 0001 2106 9910Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Benjamin R. Morehouse
- grid.38142.3c000000041936754XDepartment of Microbiology, Harvard Medical School, Boston, MA USA ,grid.65499.370000 0001 2106 9910Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Adelyn E. Ragucci
- grid.38142.3c000000041936754XDepartment of Microbiology, Harvard Medical School, Boston, MA USA ,grid.65499.370000 0001 2106 9910Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Wen Zhou
- grid.38142.3c000000041936754XDepartment of Microbiology, Harvard Medical School, Boston, MA USA ,grid.65499.370000 0001 2106 9910Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.263817.9Present Address: School of Life Sciences, Southern University of Science and Technology, Guangdong, China
| | - Xianlong Ai
- grid.410737.60000 0000 8653 1072Sino-French Hoffmann Institute, State Key Laboratory of Respiratory Disease, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Yuqiang Chen
- grid.410737.60000 0000 8653 1072Sino-French Hoffmann Institute, State Key Laboratory of Respiratory Disease, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Lihua Li
- grid.410737.60000 0000 8653 1072Sino-French Hoffmann Institute, State Key Laboratory of Respiratory Disease, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Ziming Wei
- grid.410737.60000 0000 8653 1072Sino-French Hoffmann Institute, State Key Laboratory of Respiratory Disease, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Heike Bähre
- grid.10423.340000 0000 9529 9877Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Martin König
- grid.10423.340000 0000 9529 9877Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Roland Seifert
- grid.10423.340000 0000 9529 9877Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany ,grid.10423.340000 0000 9529 9877Hannover Medical School, Institute of Pharmacology, Hannover, Germany
| | - Amy S. Y. Lee
- grid.65499.370000 0001 2106 9910Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Cell Biology, Harvard Medical School, Boston, MA USA
| | - Hua Cai
- grid.410737.60000 0000 8653 1072Sino-French Hoffmann Institute, State Key Laboratory of Respiratory Disease, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Jean-Luc Imler
- grid.410737.60000 0000 8653 1072Sino-French Hoffmann Institute, State Key Laboratory of Respiratory Disease, School of Basic Medical Science, Guangzhou Medical University, Guangzhou, China ,grid.11843.3f0000 0001 2157 9291Université de Strasbourg, CNRS UPR9022 Strasbourg, France
| | - Philip J. Kranzusch
- grid.38142.3c000000041936754XDepartment of Microbiology, Harvard Medical School, Boston, MA USA ,grid.65499.370000 0001 2106 9910Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA USA
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436
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Lin CSH, Chan ACK, Vermeulen J, Brockerman J, Soni AS, Tanner ME, Gaynor EC, McIntosh LP, Simorre JP, Murphy MEP. Peptidoglycan binding by a pocket on the accessory NTF2-domain of Pgp2 directs helical cell shape of Campylobacter jejuni. J Biol Chem 2021; 296:100528. [PMID: 33711341 PMCID: PMC8038945 DOI: 10.1016/j.jbc.2021.100528] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/01/2021] [Accepted: 03/08/2021] [Indexed: 01/25/2023] Open
Abstract
The helical morphology of Campylobacter jejuni, a bacterium involved in host gut colonization and pathogenesis in humans, is determined by the structure of the peptidoglycan (PG) layer. This structure is dictated by trimming of peptide stems by the LD-carboxypeptidase Pgp2 within the periplasm. The interaction interface between Pgp2 and PG to select sites for peptide trimming is unknown. We determined a 1.6 Å resolution crystal structure of Pgp2, which contains a conserved LD-carboxypeptidase domain and a previously uncharacterized domain with an NTF2-like fold (NTF2). We identified a pocket in the NTF2 domain formed by conserved residues and located ∼40 Å from the LD-carboxypeptidase active site. Expression of pgp2 in trans with substitutions of charged (Lys257, Lys307, Glu324) and hydrophobic residues (Phe242 and Tyr233) within the pocket did not restore helical morphology to a pgp2 deletion strain. Muropeptide analysis indicated a decrease of murotripeptides in the deletion strain expressing these mutants, suggesting reduced Pgp2 catalytic activity. Pgp2 but not the K307A mutant was pulled down by C. jejuni Δpgp2 PG sacculi, supporting a role for the pocket in PG binding. NMR spectroscopy was used to define the interaction interfaces of Pgp2 with several PG fragments, which bound to the active site within the LD-carboxypeptidase domain and the pocket of the NTF2 domain. We propose a model for Pgp2 binding to PG strands involving both the LD-carboxypeptidase domain and the accessory NTF2 domain to induce a helical cell shape.
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Affiliation(s)
- Chang Sheng-Huei Lin
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anson C K Chan
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jenny Vermeulen
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jacob Brockerman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Arvind S Soni
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin E Tanner
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Erin C Gaynor
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Michael E P Murphy
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
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437
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Liu X, Zhao M, Fan X, Fu Y. Reshaping the active pocket of esterase Est816 for resolution of economically important racemates. Catal Sci Technol 2021. [DOI: 10.1039/d1cy01028j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Eight 2-arylpropionic acids with high E values were generated by engineered Est816, which overcomes the contradiction between the wide substrate scope and high enantioselectivity of esterases.
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Affiliation(s)
- Xiaolong Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Meng Zhao
- School of Basic Medical Sciences, Anhui Medical University, 81 Meishan Rd, Hefei, 230032, Anhui, People's Republic of China
| | - Xinjiong Fan
- School of Basic Medical Sciences, Anhui Medical University, 81 Meishan Rd, Hefei, 230032, Anhui, People's Republic of China
| | - Yao Fu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Key Laboratory of Urban Pollutant Conversion, Anhui Province Key Laboratory of Biomass Clean Energy, iChEM, University of Science and Technology of China, Hefei, Anhui 230026, China
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438
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Fukuda Y, Inoue T. Structural insights into a C2 domain protein specifically found in tardigrades. Protein Sci 2020; 30:513-518. [PMID: 33226149 PMCID: PMC7784755 DOI: 10.1002/pro.4002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/14/2020] [Accepted: 11/17/2020] [Indexed: 11/17/2022]
Abstract
Some tardigrades can survive extremely desiccated conditions through transition into a state called anhydrobiosis. Anhydrobiotic tardigrades have proteins unique to them and they are thought to be keys to the understanding of unusual desiccation resistance. In fact, previous transcriptome data show that several tardigrade‐specific proteins are significantly upregulated under desiccated conditions. However, their physiological roles and chemical properties have been ambiguous because they show low or no similarity of amino acid sequences to proteins found in other organisms. Here, we report a crystal structure of one of such proteins. This protein shows a β‐sandwich structure composed of 8 β‐strands, three Ca2+‐binding sites, and hydrophobic residues on Ca2+‐binding (CBD) loops, which resemble characteristics of C2 domain proteins. We therefore conveniently describe this protein as tardigrade C2 domain protein (TC2P). Because the C2 domain functions as a Ca2+‐mediated membrane docking module, which is related to signal transduction or membrane trafficking, TC2Ps may play a role in Ca2+‐triggered phenomenon under desiccated situations. Our finding provides not only structural insights into a newly discovered desiccation‐related protein family but also insights into the evolution and diversity of C2 domain proteins. PDB Code(s): 7DF2;
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Affiliation(s)
- Yohta Fukuda
- Graduate School of Pharmaceutical Science, Osaka University, Osaka, Japan
| | - Tsuyoshi Inoue
- Graduate School of Pharmaceutical Science, Osaka University, Osaka, Japan
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439
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McGuire BE, Hettle AG, Vickers C, King DT, Vocadlo DJ, Boraston AB. The structure of a family 110 glycoside hydrolase provides insight into the hydrolysis of α-1,3-galactosidic linkages in λ-carrageenan and blood group antigens. J Biol Chem 2020; 295:18426-18435. [PMID: 33127644 PMCID: PMC7939477 DOI: 10.1074/jbc.ra120.015776] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/23/2020] [Indexed: 11/30/2022] Open
Abstract
α-Linked galactose is a common carbohydrate motif in nature that is processed by a variety of glycoside hydrolases from different families. Terminal Galα1-3Gal motifs are found as a defining feature of different blood group and tissue antigens, as well as the building block of the marine algal galactan λ-carrageenan. The blood group B antigen and linear α-Gal epitope can be processed by glycoside hydrolases in family GH110, whereas the presence of genes encoding GH110 enzymes in polysaccharide utilization loci from marine bacteria suggests a role in processing λ-carrageenan. However, the structure-function relationships underpinning the α-1,3-galactosidase activity within family GH110 remain unknown. Here we focus on a GH110 enzyme (PdGH110B) from the carrageenolytic marine bacterium Pseudoalteromonas distincta U2A. We showed that the enzyme was active on Galα1-3Gal but not the blood group B antigen. X-ray crystal structures in complex with galactose and unhydrolyzed Galα1-3Gal revealed the parallel β-helix fold of the enzyme and the structural basis of its inverting catalytic mechanism. Moreover, an examination of the active site reveals likely adaptations that allow accommodation of fucose in blood group B active GH110 enzymes or, in the case of PdGH110, accommodation of the sulfate groups found on λ-carrageenan. Overall, this work provides insight into the first member of a predominantly marine clade of GH110 enzymes while also illuminating the structural basis of α-1,3-galactoside processing by the family as a whole.
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Affiliation(s)
- Bailey E McGuire
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Andrew G Hettle
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Chelsea Vickers
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Dustin T King
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - David J Vocadlo
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada; Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Alisdair B Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
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440
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Kazakov AS, Sofin AD, Avkhacheva NV, Denesyuk AI, Deryusheva EI, Rastrygina VA, Sokolov AS, Permyakova ME, Litus EA, Uversky VN, Permyakov EA, Permyakov SE. Interferon Beta Activity Is Modulated via Binding of Specific S100 Proteins. Int J Mol Sci 2020; 21:ijms21249473. [PMID: 33322098 PMCID: PMC7764042 DOI: 10.3390/ijms21249473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/18/2022] Open
Abstract
Interferon-β (IFN-β) is a pleiotropic cytokine used for therapy of multiple sclerosis, which is also effective in suppression of viral and bacterial infections and cancer. Recently, we reported a highly specific interaction between IFN-β and S100P lowering IFN-β cytotoxicity to cancer cells (Int J Biol Macromol. 2020; 143: 633–639). S100P is a member of large family of multifunctional Ca2+-binding proteins with cytokine-like activities. To probe selectivity of IFN-β—S100 interaction with respect to S100 proteins, we used surface plasmon resonance spectroscopy, chemical crosslinking, and crystal violet assay. Among the thirteen S100 proteins studied S100A1, S100A4, and S100A6 proteins exhibit strictly Ca2+-dependent binding to IFN-β with equilibrium dissociation constants, Kd, of 0.04–1.5 µM for their Ca2+-bound homodimeric forms. Calcium depletion abolishes the S100—IFN-β interactions. Monomerization of S100A1/A4/A6 decreases Kd values down to 0.11–1.0 nM. Interferon-α is unable of binding to the S100 proteins studied. S100A1/A4 proteins inhibit IFN-β-induced suppression of MCF-7 cells viability. The revealed direct influence of specific S100 proteins on IFN-β activity uncovers a novel regulatory role of particular S100 proteins, and opens up novel approaches to enhancement of therapeutic efficacy of IFN-β.
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Affiliation(s)
- Alexey S. Kazakov
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institutskaya str., 7, 142290 Pushchino, Russia; (A.S.K.); (A.D.S.); (N.V.A.); (A.I.D.); (E.I.D.); (V.A.R.); (A.S.S.); (M.E.P.); (E.A.L.); (E.A.P.)
| | - Alexander D. Sofin
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institutskaya str., 7, 142290 Pushchino, Russia; (A.S.K.); (A.D.S.); (N.V.A.); (A.I.D.); (E.I.D.); (V.A.R.); (A.S.S.); (M.E.P.); (E.A.L.); (E.A.P.)
| | - Nadezhda V. Avkhacheva
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institutskaya str., 7, 142290 Pushchino, Russia; (A.S.K.); (A.D.S.); (N.V.A.); (A.I.D.); (E.I.D.); (V.A.R.); (A.S.S.); (M.E.P.); (E.A.L.); (E.A.P.)
| | - Alexander I. Denesyuk
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institutskaya str., 7, 142290 Pushchino, Russia; (A.S.K.); (A.D.S.); (N.V.A.); (A.I.D.); (E.I.D.); (V.A.R.); (A.S.S.); (M.E.P.); (E.A.L.); (E.A.P.)
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Evgenia I. Deryusheva
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institutskaya str., 7, 142290 Pushchino, Russia; (A.S.K.); (A.D.S.); (N.V.A.); (A.I.D.); (E.I.D.); (V.A.R.); (A.S.S.); (M.E.P.); (E.A.L.); (E.A.P.)
| | - Victoria A. Rastrygina
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institutskaya str., 7, 142290 Pushchino, Russia; (A.S.K.); (A.D.S.); (N.V.A.); (A.I.D.); (E.I.D.); (V.A.R.); (A.S.S.); (M.E.P.); (E.A.L.); (E.A.P.)
| | - Andrey S. Sokolov
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institutskaya str., 7, 142290 Pushchino, Russia; (A.S.K.); (A.D.S.); (N.V.A.); (A.I.D.); (E.I.D.); (V.A.R.); (A.S.S.); (M.E.P.); (E.A.L.); (E.A.P.)
| | - Maria E. Permyakova
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institutskaya str., 7, 142290 Pushchino, Russia; (A.S.K.); (A.D.S.); (N.V.A.); (A.I.D.); (E.I.D.); (V.A.R.); (A.S.S.); (M.E.P.); (E.A.L.); (E.A.P.)
| | - Ekaterina A. Litus
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institutskaya str., 7, 142290 Pushchino, Russia; (A.S.K.); (A.D.S.); (N.V.A.); (A.I.D.); (E.I.D.); (V.A.R.); (A.S.S.); (M.E.P.); (E.A.L.); (E.A.P.)
| | - Vladimir N. Uversky
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institutskaya str., 7, 142290 Pushchino, Russia; (A.S.K.); (A.D.S.); (N.V.A.); (A.I.D.); (E.I.D.); (V.A.R.); (A.S.S.); (M.E.P.); (E.A.L.); (E.A.P.)
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence: (V.N.U.); (S.E.P.); Tel.: +7-(495)-143-7741 (S.E.P.); Fax: +7-(4967)-33-05-22 (S.E.P.)
| | - Eugene A. Permyakov
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institutskaya str., 7, 142290 Pushchino, Russia; (A.S.K.); (A.D.S.); (N.V.A.); (A.I.D.); (E.I.D.); (V.A.R.); (A.S.S.); (M.E.P.); (E.A.L.); (E.A.P.)
| | - Sergei E. Permyakov
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institutskaya str., 7, 142290 Pushchino, Russia; (A.S.K.); (A.D.S.); (N.V.A.); (A.I.D.); (E.I.D.); (V.A.R.); (A.S.S.); (M.E.P.); (E.A.L.); (E.A.P.)
- Correspondence: (V.N.U.); (S.E.P.); Tel.: +7-(495)-143-7741 (S.E.P.); Fax: +7-(4967)-33-05-22 (S.E.P.)
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Dai L, Qin L, Hu Y, Huang JW, Hu Z, Min J, Sun Y, Guo RT. Structural dissection of unnatural ginsenoside-biosynthetic UDP-glycosyltransferase Bs-YjiC from Bacillus subtilis for substrate promiscuity. Biochem Biophys Res Commun 2020; 534:73-78. [PMID: 33310191 DOI: 10.1016/j.bbrc.2020.11.104] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/20/2022]
Abstract
Glycosylation catalyzed by uridine diphosphate-dependent glycosyltransferases (UGT) contributes to the chemical and functional diversity of a number of natural products. Bacillus subtilis Bs-YjiC is a robust and versatile UGT that holds potentials in the biosynthesis of unnatural bioactive ginsenosides. To understand the molecular mechanism underlying the substrate promiscuity of Bs-YjiC, we solved crystal structures of Bs-YjiC and its binary complex with uridine diphosphate (UDP) at resolution of 2.18 Å and 2.44 Å, respectively. Bs-YjiC adopts the classical GT-B fold containing the N-terminal and C-terminal domains that accommodate the sugar acceptor and UDP-glucose, respectively. Molecular docking indicates that the spacious sugar-acceptor binding pocket of Bs-YjiC might be responsible for its broad substrate spectrum and unique glycosylation patterns toward protopanaxadiol-(PPD) and PPD-type ginsenosides. Our study reveals the structural basis for the aglycone promiscuity of Bs-YjiC and will facilitate the protein engineering of Bs-YjiC to synthesize novel bioactive glycosylated compounds.
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Affiliation(s)
- Longhai Dai
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Lujiao Qin
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Yumei Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Jian-Wen Huang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Zheyang Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Jian Min
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China
| | - Yuanxia Sun
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, PR China.
| | - Rey-Ting Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, PR China.
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442
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Ouzounis CA. A recent origin of Orf3a from M protein across the coronavirus lineage arising by sharp divergence. Comput Struct Biotechnol J 2020; 18:4093-4102. [PMID: 33363705 PMCID: PMC7749296 DOI: 10.1016/j.csbj.2020.11.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 12/18/2022] Open
Abstract
The genome of SARS-CoV-2, the coronavirus responsible for the Covid-19 pandemic, encodes a number of accessory genes. The longest accessory gene, Orf3a, plays important roles in the virus lifecycle indicated by experimental findings, known polymorphisms, its evolutionary trajectory and a distinct three-dimensional fold. Here we show that supervised, sensitive database searches with Orf3a detect weak, yet significant and highly specific similarities to the M proteins of coronaviruses. The similarity profiles can be used to derive low-resolution three-dimensional models for M proteins based on Orf3a as a structural template. The models also explain the emergence of Orf3a from M proteins and suggest a recent origin across the coronavirus lineage, enunciated by its restricted phylogenetic distribution. This study provides evidence for the common origin of M and Orf3a families and proposes for the first time a working model for the structure of the universally distributed M proteins in coronaviruses, consistent with the properties of both protein families.
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Affiliation(s)
- Christos A. Ouzounis
- Biological Computation & Process Laboratory (BCPL), Chemical Process & Energy Resources Institute (CPERI), Centre for Research & Technology Hellas (CERTH), PO Box 361, GR-57001 Thessalonica, Greece
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443
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Tonozuka T, Kitamura J, Nagaya M, Kawai R, Nishikawa A, Hirano K, Tamura K, Fujii T, Tochio T. Crystal structure of a glycoside hydrolase family 68 β-fructosyltransferase from Beijerinckia indica subsp. indica in complex with fructose. Biosci Biotechnol Biochem 2020; 84:2508-2520. [DOI: 10.1080/09168451.2020.1804317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Abstract
An enzyme belonging to glycoside hydrolase family 68 (GH68) from Beijerinckia indica subsp. indica NBRC 3744 was expressed in Escherichia coli. Biochemical characterization showed that the enzyme was identified to be a β-fructosyltransferase (BiBftA). Crystallization of a full-length BiBftA was initially attempted, but no crystals were obtained. We constructed a variant in which 5 residues (Pro199-Gly203) and 13 residues (Leu522-Gln534) in potentially flexible regions were deleted, and we successfully crystallized this variant BiBftA. BiBftA is composed of a five-bladed β-propeller fold as in other GH68 enzymes. The structure of BiBftA in complex with fructose unexpectedly indicated that one β-fructofuranose (β-Fruf) molecule and one β-fructopyranose molecule bind to the catalytic pocket. The orientation of β-Fruf at subsite −1 is tilted from the orientation observed in most GH68 enzymes, presenting a second structure of a GH68 enzyme in complex with the tilted binding mode of β-Fruf.
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Affiliation(s)
- Takashi Tonozuka
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Junichi Kitamura
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Mika Nagaya
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Reika Kawai
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Atsushi Nishikawa
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
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444
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Maeda S, Yamamoto H, Kinch LN, Garza CM, Takahashi S, Otomo C, Grishin NV, Forli S, Mizushima N, Otomo T. Structure, lipid scrambling activity and role in autophagosome formation of ATG9A. Nat Struct Mol Biol 2020; 27:1194-1201. [PMID: 33106659 PMCID: PMC7718406 DOI: 10.1038/s41594-020-00520-2] [Citation(s) in RCA: 178] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/22/2020] [Indexed: 01/01/2023]
Abstract
De novo formation of the double-membrane compartment autophagosome is seeded by small vesicles carrying membrane protein autophagy-related 9 (ATG9), the function of which remains unknown. Here we find that ATG9A scrambles phospholipids of membranes in vitro. Cryo-EM structures of human ATG9A reveal a trimer with a solvated central pore, which is connected laterally to the cytosol through the cavity within each protomer. Similarities to ABC exporters suggest that ATG9A could be a transporter that uses the central pore to function. Moreover, molecular dynamics simulation suggests that the central pore opens laterally to accommodate lipid headgroups, thereby enabling lipids to flip. Mutations in the pore reduce scrambling activity and yield markedly smaller autophagosomes, indicating that lipid scrambling by ATG9A is essential for membrane expansion. We propose ATG9A acts as a membrane-embedded funnel to facilitate lipid flipping and to redistribute lipids added to the outer leaflet of ATG9 vesicles, thereby enabling growth into autophagosomes.
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Affiliation(s)
- Shintaro Maeda
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Hayashi Yamamoto
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Lisa N Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Christina M Garza
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Satoru Takahashi
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Neurosurgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Chinatsu Otomo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takanori Otomo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
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445
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Klein TA, Grebenc DW, Gandhi SY, Shah VS, Kim Y, Whitney JC. Structure of the Extracellular Region of the Bacterial Type VIIb Secretion System Subunit EsaA. Structure 2020; 29:177-185.e6. [PMID: 33238147 DOI: 10.1016/j.str.2020.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/17/2020] [Accepted: 11/02/2020] [Indexed: 12/15/2022]
Abstract
Gram-positive bacteria use type VII secretion systems (T7SSs) to export effector proteins that manipulate the physiology of nearby prokaryotic and eukaryotic cells. Several mycobacterial T7SSs have established roles in virulence. By contrast, the genetically distinct T7SSb pathway found in Firmicutes bacteria more often functions to mediate bacterial competition. A lack of structural information on the T7SSb has limited the understanding of effector export by this protein secretion apparatus. Here, we present the 2.4 Å crystal structure of the extracellular region of the T7SSb subunit EsaA from Streptococcus gallolyticus. Our structure reveals that homodimeric EsaA is an elongated, arrow-shaped protein with a surface-accessible "tip", which in some species of bacteria serves as a receptor for lytic bacteriophages. Because it is the only T7SSb subunit large enough to traverse the peptidoglycan layer of Firmicutes, we propose that EsaA plays a critical role in transporting effectors across the entirety of the Gram-positive cell envelope.
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Affiliation(s)
- Timothy A Klein
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Dirk W Grebenc
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Shil Y Gandhi
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Vraj S Shah
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Youngchang Kim
- Structural Biology Center, X-ray Science, Argonne National Laboratory, Argonne, IL, USA
| | - John C Whitney
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S 4K1, Canada; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON L8S 4K1, Canada.
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446
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Strayer EC, Lu S, Ribeiro J, Andersen JF. Salivary complement inhibitors from mosquitoes: Structure and mechanism of action. J Biol Chem 2020; 296:100083. [PMID: 33199367 PMCID: PMC7948415 DOI: 10.1074/jbc.ra120.015230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/12/2020] [Accepted: 11/16/2020] [Indexed: 12/20/2022] Open
Abstract
Inhibition of the alternative pathway (AP) of complement by saliva from Anopheles mosquitoes facilitates feeding by blocking production of the anaphylatoxins C3a and C5a, which activate mast cells leading to plasma extravasation, pain, and itching. We have previously shown that albicin, a member of the SG7 protein family from An. Albimanus, blocks the AP by binding to and inhibiting the function of the C3 convertase, C3bBb. Here we show that SG7.AF, the albicin homolog from An. freeborni, has a similar potency to albicin but is more active in the presence of properdin, a plasma protein that acts to stabilize C3bBb. Conversely, albicin is highly active in the absence or presence of properdin. Albicin and SG7.AF stabilize the C3bBb complex in a form that accumulates on surface plasmon resonance (SPR) surfaces coated with properdin, but SG7.AF binds with lower affinity than albicin. Albicin induces oligomerization of the complex in solution, suggesting that it is oligomerization that leads to stabilization on SPR surfaces. Anophensin, the albicin ortholog from An. stephensi, is only weakly active as an inhibitor of the AP, suggesting that the SG7 family may play a different functional role in this species and other species of the subgenus Cellia, containing the major malaria vectors in Africa and Asia. Crystal structures of albicin and SG7.AF reveal a novel four-helix bundle arrangement that is stabilized by an N-terminal hydrogen bonding network. These structures provide insight into the SG7 family and related mosquito salivary proteins including the platelet-inhibitory 30 kDa family.
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Affiliation(s)
- Ethan C Strayer
- Laboratory of Malaria and Vector Research, NIH-NIAID, Rockville, Maryland, USA
| | - Stephen Lu
- Laboratory of Malaria and Vector Research, NIH-NIAID, Rockville, Maryland, USA
| | - Jose Ribeiro
- Laboratory of Malaria and Vector Research, NIH-NIAID, Rockville, Maryland, USA
| | - John F Andersen
- Laboratory of Malaria and Vector Research, NIH-NIAID, Rockville, Maryland, USA.
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447
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Xie J, Ke M, Xu L, Lin S, Huang J, Zhang J, Yang F, Wu J, Yan Z. Structure of the human sodium leak channel NALCN in complex with FAM155A. Nat Commun 2020; 11:5831. [PMID: 33203861 PMCID: PMC7672056 DOI: 10.1038/s41467-020-19667-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 10/26/2020] [Indexed: 01/18/2023] Open
Abstract
NALCN, a sodium leak channel expressed mainly in the central nervous system, is responsible for the resting Na+ permeability that controls neuronal excitability. Dysfunctions of the NALCN channelosome, NALCN with several auxiliary subunits, are associated with a variety of human diseases. Here, we report the cryo-EM structure of human NALCN in complex with FAM155A at an overall resolution of 3.1 angstroms. FAM155A forms extensive interactions with the extracellular loops of NALCN that may help stabilize NALCN in the membrane. A Na+ ion-binding site, reminiscent of a Ca2+ binding site in Cav channels, is identified in the unique EEKE selectivity filter. Despite its 'leaky' nature, the channel is closed and the intracellular gate is sealed by S6I, II-III linker and III-IV linker. Our study establishes the molecular basis of Na+ permeation and voltage sensitivity, and provides important clues to the mechanistic understanding of NALCN regulation and NALCN channelosome-related diseases.
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Affiliation(s)
- Jiongfang Xie
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 310024, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, 310024, Hangzhou, Zhejiang, China
| | - Meng Ke
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 310024, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, 310024, Hangzhou, Zhejiang, China
| | - Lizhen Xu
- Department of Biophysics and Kidney Disease Center, First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Shiyi Lin
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 310024, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, 310024, Hangzhou, Zhejiang, China
| | - Jin Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 310024, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, 310024, Hangzhou, Zhejiang, China
| | - Jiabei Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 310024, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, 310024, Hangzhou, Zhejiang, China
| | - Fan Yang
- Department of Biophysics and Kidney Disease Center, First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
| | - Jianping Wu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 310024, Hangzhou, Zhejiang, China.
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, 310024, Hangzhou, Zhejiang, China.
| | - Zhen Yan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 310024, Hangzhou, Zhejiang, China.
- Westlake Laboratory of Life Sciences and Biomedicine, 310024, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, 310024, Hangzhou, Zhejiang, China.
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448
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Zhou J, Pecqueur L, Aučynaitė A, Fuchs J, Rutkienė R, Vaitekūnas J, Meškys R, Boll M, Fontecave M, Urbonavičius J, Golinelli-Pimpaneau B. Structural Evidence for a [4Fe-5S] Intermediate in the Non-Redox Desulfuration of Thiouracil. Angew Chem Int Ed Engl 2020; 60:424-431. [PMID: 32929873 DOI: 10.1002/anie.202011211] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Indexed: 11/10/2022]
Abstract
We recently discovered a [Fe-S]-containing protein with in vivo thiouracil desulfidase activity, dubbed TudS. The crystal structure of TudS refined at 1.5 Å resolution is reported; it harbors a [4Fe-4S] cluster bound by three cysteines only. Incubation of TudS crystals with 4-thiouracil trapped the cluster with a hydrosulfide ligand bound to the fourth non-protein-bonded iron, as established by the sulfur anomalous signal. This indicates that a [4Fe-5S] state of the cluster is a catalytic intermediate in the desulfuration reaction. Structural data and site-directed mutagenesis indicate that a water molecule is located next to the hydrosulfide ligand and to two catalytically important residues, Ser101 and Glu45. This information, together with modeling studies allow us to propose a mechanism for the unprecedented non-redox enzymatic desulfuration of thiouracil, in which a [4Fe-4S] cluster binds and activates the sulfur atom of the substrate.
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Affiliation(s)
- Jingjing Zhou
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, Paris CEDEX 05, France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, Paris CEDEX 05, France
| | - Agota Aučynaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Jonathan Fuchs
- Faculty of Biology-Microbiology, University of Freiburg, 79104, Freiburg, Germany
| | - Rasa Rutkienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Justas Vaitekūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Matthias Boll
- Faculty of Biology-Microbiology, University of Freiburg, 79104, Freiburg, Germany
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, Paris CEDEX 05, France
| | - Jaunius Urbonavičius
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania.,Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Vilnius, Lithuania
| | - Béatrice Golinelli-Pimpaneau
- Laboratoire de Chimie des Processus Biologiques, UMR 8229 CNRS, Collège de France, Sorbonne Université, Paris CEDEX 05, France
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449
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Zhang N, Chang Y, Tseng R, Ovchinnikov S, Schwarz R, LiWang A. Solution NMR structure of Se0862, a highly conserved cyanobacterial protein involved in biofilm formation. Protein Sci 2020; 29:2274-2280. [PMID: 32949024 PMCID: PMC7586914 DOI: 10.1002/pro.3952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/08/2020] [Accepted: 09/12/2020] [Indexed: 12/13/2022]
Abstract
Biofilms are accumulations of microorganisms embedded in extracellular matrices that protect against external factors and stressful environments. Cyanobacterial biofilms are ubiquitous and have potential for treatment of wastewater and sustainable production of biofuels. But the underlying mechanisms regulating cyanobacterial biofilm formation are unclear. Here, we report the solution NMR structure of a protein, Se0862, conserved across diverse cyanobacterial species and involved in regulation of biofilm formation in the cyanobacterium Synechococcus elongatus PCC 7942. Se0862 is a class α+β protein with ααββββαα topology and roll architecture, consisting of a four-stranded β-sheet that is flanked by four α-helices on one side. Conserved surface residues constitute a hydrophobic pocket and charged regions that are likely also present in Se0862 orthologs.
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Affiliation(s)
- Ning Zhang
- Department of Chemistry and Chemical BiologyUniversity of CaliforniaMercedCaliforniaUSA
| | - Yong‐Gang Chang
- Department of Chemistry and Chemical BiologyUniversity of CaliforniaMercedCaliforniaUSA
- Monash UniversityVictoriaAustralia
| | - Roger Tseng
- Department of Chemistry and Chemical BiologyUniversity of CaliforniaMercedCaliforniaUSA
- United States Department of AgricultureAmesIAUSA
| | | | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar‐Ilan UniversityRamat‐GanIsrael
| | - Andy LiWang
- Department of Chemistry and Chemical BiologyUniversity of CaliforniaMercedCaliforniaUSA
- Center for Cellular and Biomolecular MachinesUniversity of CaliforniaMercedCaliforniaUSA
- Health Sciences Research InstituteUniversity of CaliforniaMercedCaliforniaUSA
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Teles E Oliveira DM, Marroquim MSC, de Serpa Brandão RMS, da Mata Sousa LCD, das Chagas Alves Lima F, do Monte SJH, de Sousa Lima AV, Coelho AGB, Costa JMS, Ramos RM, Miranda Pereira E, da Silva AS. pHLA3D: Updating the database of predicted three-dimensional structures of HLA with HLA-DR, HLA-DQ and HLA-DP molecules. Hum Immunol 2020; 82:8-10. [PMID: 33129577 DOI: 10.1016/j.humimm.2020.10.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 01/04/2023]
Abstract
To improve the availability of three-dimensional (3D) structures of HLA molecules, we created the pHLA3D database. In its first version, we modeled and published 106 3D structures of HLA class I molecules from the HLA-A, HLA-B, and HLA-C loci. This paper presents an update of this database, providing more 127 3D structures of HLA class II molecules (41 DR, 42 DQ, and 44 DP), predicted via homology modeling with MODELLER and SWISS-MODEL. These new 3D structures of HLA class II molecules are now freely available at pHLA3D (www.phla3d.com.br) for immunologists and other researchers working with HLA molecules.
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Affiliation(s)
| | | | | | - Luiz Claudio Demes da Mata Sousa
- Laboratory of Immunogenetics and Molecular Biology, Federal University of Piauí, Teresina, PI, Brazil; Department of Computation, Federal University of Piauí, Teresina, PI, Brazil
| | - Francisco das Chagas Alves Lima
- Research Group in Computational Quantum Chemistry & Pharmaceutical Planning, State University of Piauí, Teresina, PI, Brazil; Department of Chemistry, State University of Piauí, Teresina, PI, Brazil
| | | | | | | | | | - Ricardo Martins Ramos
- Research Laboratory in Information Systems, Federal Institute of Piauí, Teresina, PI, Brazil; Department of Information, Environment, Health and Food Production, Federal Institute of Piauí, Teresina, PI, Brazil
| | - Ester Miranda Pereira
- Laboratory of Immunogenetics and Molecular Biology, Federal University of Piauí, Teresina, PI, Brazil
| | - Adalberto Socorro da Silva
- Laboratory of Immunogenetics and Molecular Biology, Federal University of Piauí, Teresina, PI, Brazil; Department of Biology, Federal University of Piauí, Teresina, PI, Brazil.
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