1
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Zhang Z, Fu J, Rack JGM, Li C, Voorneveld J, Filippov DV, Ahel I, Luo ZQ, Das C. Legionella metaeffector MavL reverses ubiquitin ADP-ribosylation via a conserved arginine-specific macrodomain. Nat Commun 2024; 15:2452. [PMID: 38503748 PMCID: PMC10951314 DOI: 10.1038/s41467-024-46649-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
ADP-ribosylation is a reversible post-translational modification involved in various cellular activities. Removal of ADP-ribosylation requires (ADP-ribosyl)hydrolases, with macrodomain enzymes being a major family in this category. The pathogen Legionella pneumophila mediates atypical ubiquitination of host targets using the SidE effector family in a process that involves ubiquitin ADP-ribosylation on arginine 42 as an obligatory step. Here, we show that the Legionella macrodomain effector MavL regulates this pathway by reversing the arginine ADP-ribosylation, likely to minimize potential detrimental effects caused by the modified ubiquitin. We determine the crystal structure of ADP-ribose-bound MavL, providing structural insights into recognition of the ADP-ribosyl group and catalytic mechanism of its removal. Further analyses reveal DUF4804 as a class of MavL-like macrodomain enzymes whose representative members show unique selectivity for mono-ADP-ribosylated arginine residue in synthetic substrates. We find such enzymes are also present in eukaryotes, as exemplified by two previously uncharacterized (ADP-ribosyl)hydrolases in Drosophila melanogaster. Crystal structures of several proteins in this class provide insights into arginine specificity and a shared mode of ADP-ribose interaction distinct from previously characterized macrodomains. Collectively, our study reveals a new regulatory layer of SidE-catalyzed ubiquitination and expands the current understanding of macrodomain enzymes.
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Affiliation(s)
- Zhengrui Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Jiaqi Fu
- Department of Biological Sciences, Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Johannes Gregor Matthias Rack
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, Oxford, UK
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, EX4 4QD, Exeter, UK
| | - Chuang Li
- Department of Biological Sciences, Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Jim Voorneveld
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Dmitri V Filippov
- Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, Oxford, UK
| | - Zhao-Qing Luo
- Department of Biological Sciences, Purdue Institute for Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, 47907, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
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2
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Hernández-Prieto JH, Martini VP, Iulek J. Structure of glyceraldehyde-3-phosphate dehydrogenase from Paracoccidioides lutzii in complex with an aldonic sugar acid. Biochimie 2024; 218:20-33. [PMID: 37709188 DOI: 10.1016/j.biochi.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 07/23/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
The pathogen Paracoccidioides lutzii (Pb01) is found in South America countries Colombia, Ecuador, Venezuela and Brazil, especially in the central, west, and north regions of the latter. It belongs to the Ajellomycetaceae family, Onygenales order, and is typically thermodimorphic, presenting yeast cells when it grows in animal tissues, but mycelia when in the environment, where it produces the infectious propagule. This fungus is one of the etiologic agents of Paracoccidioidomycosis (PCM), the most important endemic fungal infection in Latin America. Investigations on its genome have contributed to a better understanding about its metabolism and revealed the complexity of several metabolic glycolytic pathways. Glyceraldehyde-3-Phosphate Dehydrogenase from Paracoccidioides lutzii (PlGAPDH) is considered a moonlighting protein and participates in several biological processes of this pathogen. The enzyme was expressed and purified, as seen in SDS-PAGE gel, crystallized and had its three dimensional structure (3D) determined in complex with NAD+, a sulphate ion and d-galactonic acid, therefore, a type of 'GAA site'. It is the first GAPDH structure to show this chemical type in this site and how this protein can bind an acid derived from oxidation of a linear hexose.
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Affiliation(s)
| | | | - Jorge Iulek
- Department of Chemistry, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil.
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3
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Yu DS, Outram MA, Smith A, McCombe CL, Khambalkar PB, Rima SA, Sun X, Ma L, Ericsson DJ, Jones DA, Williams SJ. The structural repertoire of Fusarium oxysporum f. sp. lycopersici effectors revealed by experimental and computational studies. eLife 2024; 12:RP89280. [PMID: 38411527 PMCID: PMC10942635 DOI: 10.7554/elife.89280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
Plant pathogens secrete proteins, known as effectors, that function in the apoplast or inside plant cells to promote virulence. Effector recognition by cell-surface or cytosolic receptors results in the activation of defence pathways and plant immunity. Despite their importance, our general understanding of fungal effector function and recognition by immunity receptors remains poor. One complication often associated with effectors is their high sequence diversity and lack of identifiable sequence motifs precluding prediction of structure or function. In recent years, several studies have demonstrated that fungal effectors can be grouped into structural classes, despite significant sequence variation and existence across taxonomic groups. Using protein X-ray crystallography, we identify a new structural class of effectors hidden within the secreted in xylem (SIX) effectors from Fusarium oxysporum f. sp. lycopersici (Fol). The recognised effectors Avr1 (SIX4) and Avr3 (SIX1) represent the founding members of the Fol dual-domain (FOLD) effector class, with members containing two distinct domains. Using AlphaFold2, we predicted the full SIX effector repertoire of Fol and show that SIX6 and SIX13 are also FOLD effectors, which we validated experimentally for SIX6. Based on structural prediction and comparisons, we show that FOLD effectors are present within three divisions of fungi and are expanded in pathogens and symbionts. Further structural comparisons demonstrate that Fol secretes effectors that adopt a limited number of structural folds during infection of tomato. This analysis also revealed a structural relationship between transcriptionally co-regulated effector pairs. We make use of the Avr1 structure to understand its recognition by the I receptor, which leads to disease resistance in tomato. This study represents an important advance in our understanding of Fol-tomato, and by extension plant-fungal interactions, which will assist in the development of novel control and engineering strategies to combat plant pathogens.
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Affiliation(s)
- Daniel S Yu
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Megan A Outram
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Ashley Smith
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Carl L McCombe
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Pravin B Khambalkar
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Sharmin A Rima
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Xizhe Sun
- Research School of Biology, The Australian National UniversityCanberraAustralia
- Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agriculture UniversityBaodingChina
| | - Lisong Ma
- Research School of Biology, The Australian National UniversityCanberraAustralia
- State Key Laboratory of North China Crop Improvement and Regulation, College of Horticulture, Hebei Agricultural UniversityBaodingChina
| | - Daniel J Ericsson
- Research School of Biology, The Australian National UniversityCanberraAustralia
- The Australian Nuclear Science and Technology Organisation, Australian SynchrotronClaytonAustralia
| | - David A Jones
- Research School of Biology, The Australian National UniversityCanberraAustralia
| | - Simon J Williams
- Research School of Biology, The Australian National UniversityCanberraAustralia
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4
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Dodge GJ, Anderson AJ, He Y, Liu W, Viner R, Imperiali B. Mapping the architecture of the initiating phosphoglycosyl transferase from S. enterica O-antigen biosynthesis in a liponanoparticle. eLife 2024; 12:RP91125. [PMID: 38358918 PMCID: PMC10942596 DOI: 10.7554/elife.91125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024] Open
Abstract
Bacterial cell surface glycoconjugates are critical for cell survival and for interactions between bacteria and their hosts. Consequently, the pathways responsible for their biosynthesis have untapped potential as therapeutic targets. The localization of many glycoconjugate biosynthesis enzymes to the membrane represents a significant challenge for expressing, purifying, and characterizing these enzymes. Here, we leverage cutting-edge detergent-free methods to stabilize, purify, and structurally characterize WbaP, a phosphoglycosyl transferase (PGT) from the Salmonella enterica (LT2) O-antigen biosynthesis. From a functional perspective, these studies establish WbaP as a homodimer, reveal the structural elements responsible for dimerization, shed light on the regulatory role of a domain of unknown function embedded within WbaP, and identify conserved structural motifs between PGTs and functionally unrelated UDP-sugar dehydratases. From a technological perspective, the strategy developed here is generalizable and provides a toolkit for studying other classes of small membrane proteins embedded in liponanoparticles beyond PGTs.
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Affiliation(s)
- Greg J Dodge
- Department of Biology and Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Alyssa J Anderson
- Department of Biology and Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Yi He
- Thermo Fisher ScientificSan JoseUnited States
| | - Weijing Liu
- Thermo Fisher ScientificSan JoseUnited States
| | - Rosa Viner
- Thermo Fisher ScientificSan JoseUnited States
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
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5
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Liu J, Corroyer-Dulmont S, Pražák V, Khusainov I, Bahrami K, Welsch S, Vasishtan D, Obarska-Kosińska A, Thorkelsson SR, Grünewald K, Quemin ERJ, Turoňová B, Locker JK. The palisade layer of the poxvirus core is composed of flexible A10 trimers. Nat Struct Mol Biol 2024:10.1038/s41594-024-01218-5. [PMID: 38316878 DOI: 10.1038/s41594-024-01218-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024]
Abstract
Due to its asymmetric shape, size and compactness, the structure of the infectious mature virus (MV) of vaccinia virus (VACV), the best-studied poxvirus, remains poorly understood. Instead, subviral particles, in particular membrane-free viral cores, have been studied with cryo-electron microscopy. Here, we compared viral cores obtained by detergent stripping of MVs with cores in the cellular cytoplasm, early in infection. We focused on the prominent palisade layer on the core surface, combining cryo-electron tomography, subtomogram averaging and AlphaFold2 structure prediction. We showed that the palisade is composed of densely packed trimers of the major core protein A10. Trimers display a random order and their classification indicates structural flexibility. A10 on cytoplasmic cores is organized in a similar manner, indicating that the structures obtained in vitro are physiologically relevant. We discuss our results in the context of the VACV replicative cycle, and the assembly and disassembly of the infectious MV.
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Affiliation(s)
- Jiasui Liu
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Simon Corroyer-Dulmont
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany
- University of Hamburg, Hamburg, Germany
| | - Vojtěch Pražák
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Iskander Khusainov
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Karola Bahrami
- Electron Microscopy of Pathogens, Paul Ehrlich Institute, Langen, Germany
- University Clinic Frankfurt, Frankfurt am Main, Germany
| | - Sonja Welsch
- Max Planck Institute of Biophysics, Central Electron Microscopy Facility, Frankfurt am Main, Germany
| | - Daven Vasishtan
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany
- Department of Biochemistry, University of Oxford, Oxford, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Sigurdur R Thorkelsson
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Kay Grünewald
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany.
- University of Hamburg, Hamburg, Germany.
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Emmanuelle R J Quemin
- Centre for Structural Systems Biology, Leibniz Institute of Virology, Hamburg, Germany.
- Department of Virology, Institute for Integrative Biology of the Cell (I2BC), CNRS UMR9198, Université Paris-Saclay, CEA, Gif-sur-Yvette, France.
| | - Beata Turoňová
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Jacomina Krijnse Locker
- Electron Microscopy of Pathogens, Paul Ehrlich Institute, Langen, Germany.
- Justus Liebig University of Giessen, Giessen, Germany.
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6
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Datler J, Hansen JM, Thader A, Schlögl A, Bauer LW, Hodirnau VV, Schur FKM. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nat Struct Mol Biol 2024:10.1038/s41594-023-01201-6. [PMID: 38316877 DOI: 10.1038/s41594-023-01201-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 12/06/2023] [Indexed: 02/07/2024]
Abstract
Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses.
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Affiliation(s)
- Julia Datler
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Jesse M Hansen
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Andreas Thader
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Alois Schlögl
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Lukas W Bauer
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | | | - Florian K M Schur
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
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7
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Chen EA, Porter LL. SSDraw: Software for generating comparative protein secondary structure diagrams. Protein Sci 2023; 32:e4836. [PMID: 37953705 PMCID: PMC10680343 DOI: 10.1002/pro.4836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/18/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023]
Abstract
The program SSDraw generates publication-quality protein secondary structure diagrams from three-dimensional protein structures. To depict relationships between secondary structure and other protein features, diagrams can be colored by conservation score, B-factor, or custom scoring. Diagrams of homologous proteins can be registered according to an input multiple sequence alignment. Linear visualization allows the user to stack registered diagrams, facilitating comparison of secondary structure and other properties among homologous proteins. SSDraw can be used to compare secondary structures of homologous proteins with both conserved and divergent folds. It can also generate one secondary structure diagram from an input protein structure of interest. The source code can be downloaded (https://github.com/ncbi/SSDraw) and run locally for rapid structure generation, while a Google Colab notebook allows easy use.
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Affiliation(s)
- Ethan A. Chen
- National Center for Biotechnology Information, National Library of MedicineNational Institutes of HealthBethesdaMarylandUSA
| | - Lauren L. Porter
- National Center for Biotechnology Information, National Library of MedicineNational Institutes of HealthBethesdaMarylandUSA
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood InstituteNational Institutes of HealthBethesdaMarylandUSA
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8
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Chen EA, Porter LL. SSDraw: software for generating comparative protein secondary structure diagrams. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554905. [PMID: 37786684 PMCID: PMC10541582 DOI: 10.1101/2023.08.25.554905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The program SSDraw generates publication-quality protein secondary structure diagrams from three-dimensional protein structures. To depict relationships between secondary structure and other protein features, diagrams can be colored by conservation score, B-factor, or custom scoring. Diagrams of homologous proteins can be registered according to an input multiple sequence alignment. Linear visualization allows the user to stack registered diagrams, facilitating comparison of secondary structure and other properties among homologous proteins. SSDraw can be used to compare secondary structures of homologous proteins with both conserved and divergent folds. It can also generate one secondary structure diagram from an input protein structure of interest. The source code can be downloaded (https://github.com/ethanchen1301/SSDraw) and run locally for rapid structure generation, while a Google Colab notebook allows easy use.
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Affiliation(s)
- Ethan A. Chen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Lauren L. Porter
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892
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9
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Teixeira Nunes M, Retailleau P, Raoux-Barbot D, Comisso M, Missinou AA, Velours C, Plancqueel S, Ladant D, Mechold U, Renault L. Functional and structural insights into the multi-step activation and catalytic mechanism of bacterial ExoY nucleotidyl cyclase toxins bound to actin-profilin. PLoS Pathog 2023; 19:e1011654. [PMID: 37747912 PMCID: PMC10553838 DOI: 10.1371/journal.ppat.1011654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 10/05/2023] [Accepted: 09/01/2023] [Indexed: 09/27/2023] Open
Abstract
ExoY virulence factors are members of a family of bacterial nucleotidyl cyclases (NCs) that are activated by specific eukaryotic cofactors and overproduce cyclic purine and pyrimidine nucleotides in host cells. ExoYs act as actin-activated NC toxins. Here, we explore the Vibrio nigripulchritudo Multifunctional-Autoprocessing Repeats-in-ToXin (MARTX) ExoY effector domain (Vn-ExoY) as a model for ExoY-type members that interact with monomeric (G-actin) instead of filamentous (F-actin) actin. Vn-ExoY exhibits moderate binding affinity to free or profilin-bound G-actin but can capture the G-actin:profilin complex, preventing its spontaneous or VASP- or formin-mediated assembly at F-actin barbed ends in vitro. This mechanism may prolong the activated cofactor-bound state of Vn-ExoY at sites of active actin cytoskeleton remodelling. We present a series of high-resolution crystal structures of nucleotide-free, 3'-deoxy-ATP- or 3'-deoxy-CTP-bound Vn-ExoY, activated by free or profilin-bound G-actin-ATP/-ADP, revealing that the cofactor only partially stabilises the nucleotide-binding pocket (NBP) of NC toxins. Substrate binding induces a large, previously-unidentified, closure of their NBP, confining catalytically important residues and metal cofactors around the substrate, and facilitating the recruitment of two metal ions to tightly coordinate the triphosphate moiety of purine or pyrimidine nucleotide substrates. We validate critical residues for both the purinyl and pyrimidinyl cyclase activity of NC toxins in Vn-ExoY and its distantly-related ExoY from Pseudomonas aeruginosa, which specifically interacts with F-actin. The data conclusively demonstrate that NC toxins employ a similar two-metal-ion mechanism for catalysing the cyclisation of nucleotides of different sizes. These structural insights into the dynamics of the actin-binding interface of actin-activated ExoYs and the multi-step activation of all NC toxins offer new perspectives for the specific inhibition of class II bacterial NC enzymes.
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Affiliation(s)
- Magda Teixeira Nunes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Pascal Retailleau
- Université Paris Saclay, CNRS, Institut de Chimie des Substances Naturelles, Gif-sur-Yvette, France
| | - Dorothée Raoux-Barbot
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unité de Biochimie des Interactions macromoléculaires, Département de Biologie Structurale et Chimie, Paris, France
| | - Martine Comisso
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Anani Amegan Missinou
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Christophe Velours
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Stéphane Plancqueel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Daniel Ladant
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unité de Biochimie des Interactions macromoléculaires, Département de Biologie Structurale et Chimie, Paris, France
| | - Undine Mechold
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unité de Biochimie des Interactions macromoléculaires, Département de Biologie Structurale et Chimie, Paris, France
| | - Louis Renault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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10
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Dodge GJ, Anderson AJ, He Y, Liu W, Viner R, Imperiali B. Mapping the architecture of the initiating phosphoglycosyl transferase from S. enterica O-antigen biosynthesis in a liponanoparticle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545297. [PMID: 37398332 PMCID: PMC10312794 DOI: 10.1101/2023.06.16.545297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Bacterial cell surface glycoconjugates are critical for cell survival and for interactions between bacteria and their hosts. Consequently, the pathways responsible for their biosynthesis have untapped potential as therapeutic targets. The localization of many glycoconjugate biosynthesis enzymes to the membrane represents a significant challenge for expressing, purifying, and characterizing these enzymes. Here, we leverage cutting-edge methods to stabilize, purify, and structurally characterize WbaP, a phosphoglycosyl transferase (PGT) from Salmonella enterica (LT2) O-antigen biosynthesis without detergent solubilization from the lipid bilayer. From a functional perspective, these studies establish WbaP as a homodimer, reveal the structural elements responsible for oligomerization, shed light on the regulatory role of a domain of unknown function embedded within WbaP, and identify conserved structural motifs between PGTs and functionally unrelated UDP-sugar dehydratases. From a technological perspective, the strategy developed here is generalizable and provides a toolkit for studying small membrane proteins embedded in liponanoparticles beyond PGTs.
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Affiliation(s)
- Greg J. Dodge
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Alyssa J. Anderson
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yi He
- Thermo Fisher Scientific, San Jose CA 95134, USA
| | - Weijing Liu
- Thermo Fisher Scientific, San Jose CA 95134, USA
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose CA 95134, USA
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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11
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Liu S, Chen H, Yin Y, Lu D, Gao G, Li J, Bai XC, Zhang X. Inhibition of FAM46/TENT5 activity by BCCIPα adopting a unique fold. SCIENCE ADVANCES 2023; 9:eadf5583. [PMID: 37018411 PMCID: PMC10075960 DOI: 10.1126/sciadv.adf5583] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
The FAM46 (also known as TENT5) proteins are noncanonical poly(A) polymerases (PAPs) implicated in regulating RNA stability. The regulatory mechanisms of FAM46 are poorly understood. Here, we report that the nuclear protein BCCIPα, but not the alternatively spliced isoform BCCIPβ, binds FAM46 and inhibits their PAP activity. Unexpectedly, our structures of the FAM46A/BCCIPα and FAM46C/BCCIPα complexes show that, despite sharing most of the sequence and differing only at the C-terminal portion, BCCIPα adopts a unique structure completely different from BCCIPβ. The distinct C-terminal segment of BCCIPα supports the adoption of the unique fold but does not directly interact with FAM46. The β sheets in BCCIPα and FAM46 pack side by side to form an extended β sheet. A helix-loop-helix segment in BCCIPα inserts into the active site cleft of FAM46, thereby inhibiting the PAP activity. Our results together show that the unique fold of BCCIPα underlies its interaction with and functional regulation of FAM46.
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Affiliation(s)
- Shun Liu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hua Chen
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Yin
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Defen Lu
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guoming Gao
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jie Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xuewu Zhang
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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12
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Wang H, Salaipeth L, Miyazaki N, Suzuki N, Okamoto K. Capsid structure of a fungal dsRNA megabirnavirus reveals its previously unidentified surface architecture. PLoS Pathog 2023; 19:e1011162. [PMID: 36848381 PMCID: PMC9997902 DOI: 10.1371/journal.ppat.1011162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/09/2023] [Accepted: 01/25/2023] [Indexed: 03/01/2023] Open
Abstract
Rosellinia necatrix megabirnavirus 1-W779 (RnMBV1) is a non-enveloped icosahedral double-stranded (ds)RNA virus that infects the ascomycete fungus Rosellinia necatrix, a causative agent that induces a lethal plant disease white root rot. Herein, we have first resolved the atomic structure of the RnMBV1 capsid at 3.2 Å resolution using cryo-electron microscopy (cryo-EM) single-particle analysis. Compared with other non-enveloped icosahedral dsRNA viruses, the RnMBV1 capsid protein structure exhibits an extra-long C-terminal arm and a surface protrusion domain. In addition, the previously unrecognized crown proteins are identified in a symmetry-expanded cryo-EM model and are present over the 3-fold axes. These exclusive structural features of the RnMBV1 capsid could have been acquired for playing essential roles in transmission and/or particle assembly of the megabirnaviruses. Our findings, therefore, will reinforce the understanding of how the structural and molecular machineries of the megabirnaviruses influence the virulence of the disease-related ascomycete fungus.
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Affiliation(s)
- Han Wang
- The Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Lakha Salaipeth
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Naoyuki Miyazaki
- Life Science Center of Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan
- * E-mail: (NM); (NS); (KO)
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
- * E-mail: (NM); (NS); (KO)
| | - Kenta Okamoto
- The Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- * E-mail: (NM); (NS); (KO)
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13
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Gruszczyk J, Grandvuillemin L, Lai-Kee-Him J, Paloni M, Savva CG, Germain P, Grimaldi M, Boulahtouf A, Kwong HS, Bous J, Ancelin A, Bechara C, Barducci A, Balaguer P, Bourguet W. Cryo-EM structure of the agonist-bound Hsp90-XAP2-AHR cytosolic complex. Nat Commun 2022; 13:7010. [PMID: 36385050 PMCID: PMC9668932 DOI: 10.1038/s41467-022-34773-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/07/2022] [Indexed: 11/17/2022] Open
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates a broad spectrum of (patho)physiological processes in response to numerous substances including pollutants, natural products and metabolites. However, the scarcity of structural data precludes understanding of how AHR is activated by such diverse compounds. Our 2.85 Å structure of the human indirubin-bound AHR complex with the chaperone Hsp90 and the co-chaperone XAP2, reported herein, reveals a closed conformation Hsp90 dimer with AHR threaded through its lumen and XAP2 serving as a brace. Importantly, we disclose the long-awaited structure of the AHR PAS-B domain revealing a unique organisation of the ligand-binding pocket and the structural determinants of ligand-binding specificity and promiscuity of the receptor. By providing structural details of the molecular initiating event leading to AHR activation, our study rationalises almost forty years of biochemical data and provides a framework for future mechanistic studies and structure-guided drug design.
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Affiliation(s)
- Jakub Gruszczyk
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France.
| | - Loïc Grandvuillemin
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Josephine Lai-Kee-Him
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Matteo Paloni
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Christos G Savva
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester, UK
| | - Pierre Germain
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Marina Grimaldi
- IRCM (Institut de Recherche en Cancérologie de Montpellier), Inserm U1194, Univ Montpellier, ICM, Montpellier, France
| | - Abdelhay Boulahtouf
- IRCM (Institut de Recherche en Cancérologie de Montpellier), Inserm U1194, Univ Montpellier, ICM, Montpellier, France
| | - Hok-Sau Kwong
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Julien Bous
- Section of Receptor Biology & Signaling, Department of Physiology & Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Aurélie Ancelin
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Cherine Bechara
- IGF, University of Montpellier, CNRS, Inserm, Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Alessandro Barducci
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Patrick Balaguer
- IRCM (Institut de Recherche en Cancérologie de Montpellier), Inserm U1194, Univ Montpellier, ICM, Montpellier, France
| | - William Bourguet
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France.
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14
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Van V, Ejimogu NE, Bui TS, Smith AT. The Structure of Saccharomyces cerevisiae Arginyltransferase 1 (ATE1). J Mol Biol 2022; 434:167816. [PMID: 36087779 PMCID: PMC9992452 DOI: 10.1016/j.jmb.2022.167816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/29/2022] [Accepted: 09/04/2022] [Indexed: 10/31/2022]
Abstract
Eukaryotic post-translational arginylation, mediated by the family of enzymes known as the arginyltransferases (ATE1s), is an important post-translational modification that can alter protein function and even dictate cellular protein half-life. Multiple major biological pathways are linked to the fidelity of this process, including neural and cardiovascular developments, cell division, and even the stress response. Despite this significance, the structural, mechanistic, and regulatory mechanisms that govern ATE1 function remain enigmatic. To that end, we have used X-ray crystallography to solve the crystal structure of ATE1 from the model organism Saccharomyces cerevisiae ATE1 (ScATE1) in the apo form. The three-dimensional structure of ScATE1 reveals a bilobed protein containing a GCN5-related N-acetyltransferase (GNAT) fold, and this crystalline behavior is faithfully recapitulated in solution based on size-exclusion chromatography-coupled small angle X-ray scattering (SEC-SAXS) analyses and cryo-EM 2D class averaging. Structural superpositions and electrostatic analyses point to this domain and its domain-domain interface as the location of catalytic activity and tRNA binding, and these comparisons strongly suggest a mechanism for post-translational arginylation. Additionally, our structure reveals that the N-terminal domain, which we have previously shown to bind a regulatory [Fe-S] cluster, is dynamic and disordered in the absence of metal bound in this location, hinting at the regulatory influence of this region. When taken together, these insights bring us closer to answering pressing questions regarding the molecular-level mechanism of eukaryotic post-translational arginylation.
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Affiliation(s)
- Verna Van
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA. https://twitter.com/VernaVan
| | - Nna-Emeka Ejimogu
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Toan S Bui
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Aaron T Smith
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA.
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15
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Chaves Rabelo N, Gomes ME, de Oliveira Moraes I, Cantagalli Pfisterer J, Loss de Morais G, Antunes D, Caffarena ER, Llerena Jr J, Gonzalez S. RASopathy Cohort of Patients Enrolled in a Brazilian Reference Center for Rare Diseases: A Novel Familial LZTR1 Variant and Recurrent Mutations. Appl Clin Genet 2022; 15:153-170. [PMID: 36304179 PMCID: PMC9595068 DOI: 10.2147/tacg.s372761] [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: 05/07/2022] [Accepted: 09/03/2022] [Indexed: 11/05/2022] Open
Abstract
Purpose Noonan syndrome and related disorders are genetic conditions affecting 1:1000-2000 individuals. Variants causing hyperactivation of the RAS/MAPK pathway lead to phenotypic overlap between syndromes, in addition to an increased risk of pediatric tumors. DNA sequencing methods have been optimized to provide a molecular diagnosis for clinical and genetic heterogeneity conditions. This work aimed to investigate the genetic basis in RASopathy patients through Next Generation Sequencing in a Reference Center for Rare Diseases (IFF/Fiocruz) and implement the precision medicine at a public health institute in Brazil. Patients and Methods This study comprises 26 cases with clinical suspicion of RASopathies. Sanger sequencing was used to screen variants in exons usually affected in the PTPN11 and HRAS genes for cases with clinical features of Noonan and Costello syndrome, respectively. Posteriorly, negative and new cases with clinical suspicion of RASopathy were analyzed by clinical or whole-exome sequencing. Results Molecular analysis revealed recurrent variants and a novel LZTR1 missense variant: 24 unrelated individuals with pathogenic variants [PTPN11(11), NF1(2), SOS1(2), SHOC2(2), HRAS(1), BRAF(1), LZTR (1), RAF1(1), KRAS(1), RIT1(1), a patient with co-occurrence of PTPN11 and NF1 mutations (1)]; familial cases carrying a known pathogenic variant in PTPN11 (mother-two children), and a previously undescribed paternally inherited variant in LZTR1. The comparative modeling analysis of the novel LZTR1 variant p.Pro225Leu showed local and global changes in the secondary and tertiary structures, showing a decrease of about 1% in the β-sheet content. Furthermore, evolutionary conservation indicated that Pro225 is in a highly conserved region, as observed for known dominant pathogenic variants in this protein. Conclusion Bringing precision medicine through NGS towards congenital syndromes promotes a better understanding of complex clinical and/or undiagnosed cases. The National Policy for Rare Diseases in Brazil emphasizes the importance of incorporating and optimizing diagnostic methodologies in the Unified Brazilian Health System (SUS). Therefore, this work is an important step for the NGS inclusion in diagnostic genetic routine in the public health system.
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Affiliation(s)
- Natana Chaves Rabelo
- Centro de Genética Médica IFF/Fiocruz, Rio de Janeiro, RJ, Brazil,Centro de Referência para Doenças Raras IFF/Fiocruz, Rio de Janeiro, RJ, Brazil,Laboratório de Medicina Genômica IFF/Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Maria Eduarda Gomes
- Centro de Genética Médica IFF/Fiocruz, Rio de Janeiro, RJ, Brazil,Centro de Referência para Doenças Raras IFF/Fiocruz, Rio de Janeiro, RJ, Brazil,Laboratório de Medicina Genômica IFF/Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Isabelle de Oliveira Moraes
- Centro de Genética Médica IFF/Fiocruz, Rio de Janeiro, RJ, Brazil,Centro de Referência para Doenças Raras IFF/Fiocruz, Rio de Janeiro, RJ, Brazil,Laboratório de Medicina Genômica IFF/Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Juliana Cantagalli Pfisterer
- Centro de Genética Médica IFF/Fiocruz, Rio de Janeiro, RJ, Brazil,Centro de Referência para Doenças Raras IFF/Fiocruz, Rio de Janeiro, RJ, Brazil,Laboratório de Medicina Genômica IFF/Fiocruz, Rio de Janeiro, RJ, Brazil
| | | | - Deborah Antunes
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz/Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Ernesto Raúl Caffarena
- Grupo de Biofísica Computacional e Modelagem Molecular, Programa de Computação Científica, Fundação Oswaldo Cruz/Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Juan Llerena Jr
- Centro de Genética Médica IFF/Fiocruz, Rio de Janeiro, RJ, Brazil,Centro de Referência para Doenças Raras IFF/Fiocruz, Rio de Janeiro, RJ, Brazil,Faculdade de Medicina de Petrópolis, FASE, Petrópolis, RJ, Brazil,INAGEMP, Rio de Janeiro, RJ, Brazil,Correspondence: Juan Llerena Jr, Email
| | - Sayonara Gonzalez
- Centro de Genética Médica IFF/Fiocruz, Rio de Janeiro, RJ, Brazil,Centro de Referência para Doenças Raras IFF/Fiocruz, Rio de Janeiro, RJ, Brazil,Laboratório de Medicina Genômica IFF/Fiocruz, Rio de Janeiro, RJ, Brazil
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16
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Mondal S, Singh SP. New insights on thioredoxins (Trxs) and glutaredoxins (Grxs) by in silico amino acid sequence, phylogenetic and comparative structural analyses in organisms of three domains of life. Heliyon 2022; 8:e10776. [PMID: 36203893 PMCID: PMC9529593 DOI: 10.1016/j.heliyon.2022.e10776] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/03/2022] [Accepted: 09/22/2022] [Indexed: 11/04/2022] Open
Abstract
Thioredoxins (Trxs) and Glutaredoxins (Grxs) regulate several cellular processes by controlling the redox state of their target proteins. Trxs and Grxs belong to thioredoxin superfamily and possess characteristic Trx/Grx fold. Several phylogenetic, biochemical and structural studies have contributed to our overall understanding of Trxs and Grxs. However, comparative study of closely related Trxs and Grxs in organisms of all domains of life was missing. Here, we conducted in silico comparative structural analysis combined with amino acid sequence and phylogenetic analyses of 65 Trxs and 88 Grxs from 12 organisms of three domains of life to get insights into evolutionary and structural relationship of two proteins. Outcomes suggested that despite diversity in their amino acids composition in distantly related organisms, both Trxs and Grxs strictly conserved functionally and structurally important residues. Also, position of these residues was highly conserved in all studied Trxs and Grxs. Notably, if any substitution occurred during evolution, preference was given to amino acids having similar chemical properties. Trxs and Grxs were found more different in eukaryotes than prokaryotes due to altered helical conformation. The surface of Trxs was negatively charged, while Grxs surface was positively charged, however, the active site was constituted by uncharged amino acids in both proteins. Also, phylogenetic analysis of Trxs and Grxs in three domains of life supported endosymbiotic origins of chloroplast and mitochondria, and suggested their usefulness in molecular systematics. We also report previously unknown catalytic motifs of two proteins, and discuss in detail about effect of abovementioned parameters on overall structural and functional diversity of Trxs and Grxs.
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17
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Dade CM, Douzi B, Cambillau C, Ball G, Voulhoux R, Forest KT. The crystal structure of CbpD clarifies substrate-specificity motifs in chitin-active lytic polysaccharide monooxygenases. Acta Crystallogr D Struct Biol 2022; 78:1064-1078. [PMID: 35916229 PMCID: PMC9344471 DOI: 10.1107/s2059798322007033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 07/08/2022] [Indexed: 11/23/2022] Open
Abstract
The 3 Å resolution crystal structure of the Pseudomonas aeruginosa virulence factor CbpD both supports and challenges the current model of how lytic polysaccharide monooxygenases bind chitin and raises interesting possibilities about how type 2 secretion-system substrates may interact with the secretion machinery. This structure also demonstrates the utility of new, AI-powered, protein structure-prediction algorithms in making challenging structural targets tractable. Pseudomonas aeruginosa secretes diverse proteins via its type 2 secretion system, including a 39 kDa chitin-binding protein, CbpD. CbpD has recently been shown to be a lytic polysaccharide monooxygenase active on chitin and to contribute substantially to virulence. To date, no structure of this virulence factor has been reported. Its first two domains are homologous to those found in the crystal structure of Vibrio cholerae GbpA, while the third domain is homologous to the NMR structure of the CBM73 domain of Cellvibrio japonicusCjLPMO10A. Here, the 3.0 Å resolution crystal structure of CbpD solved by molecular replacement is reported, which required ab initio models of each CbpD domain generated by the artificial intelligence deep-learning structure-prediction algorithm RoseTTAFold. The structure of CbpD confirms some previously reported substrate-specificity motifs among LPMOAA10s, while challenging the predictive power of others. Additionally, the structure of CbpD shows that post-translational modifications occur on the chitin-binding surface. Moreover, the structure raises interesting possibilities about how type 2 secretion-system substrates may interact with the secretion machinery and demonstrates the utility of new artificial intelligence protein structure-prediction algorithms in making challenging structural targets tractable.
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18
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Sacco MD, Wang S, Adapa SR, Zhang X, Lewandowski EM, Gongora MV, Keramisanou D, Atlas ZD, Townsend JA, Gatdula JR, Morgan RT, Hammond LR, Marty MT, Wang J, Eswara PJ, Gelis I, Jiang RHY, Sun X, Chen Y. A unique class of Zn 2+-binding serine-based PBPs underlies cephalosporin resistance and sporogenesis in Clostridioides difficile. Nat Commun 2022; 13:4370. [PMID: 35902581 PMCID: PMC9334274 DOI: 10.1038/s41467-022-32086-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 07/18/2022] [Indexed: 11/17/2022] Open
Abstract
Treatment with β-lactam antibiotics, particularly cephalosporins, is a major risk factor for Clostridioides difficile infection. These broad-spectrum antibiotics irreversibly inhibit penicillin-binding proteins (PBPs), which are serine-based enzymes that assemble the bacterial cell wall. However, C. difficile has four different PBPs (PBP1-3 and SpoVD) with various roles in growth and spore formation, and their specific links to β-lactam resistance in this pathogen are underexplored. Here, we show that PBP2 (known to be essential for vegetative growth) is the primary bactericidal target for β-lactams in C. difficile. PBP2 is insensitive to cephalosporin inhibition, and this appears to be the main basis for cephalosporin resistance in this organism. We determine crystal structures of C. difficile PBP2, alone and in complex with β-lactams, revealing unique features including ligand-induced conformational changes and an active site Zn2+-binding motif that influences β-lactam binding and protein stability. The Zn2+-binding motif is also present in C. difficile PBP3 and SpoVD (which are known to be essential for sporulation), as well as in other bacterial taxa including species living in extreme environments and the human gut. We speculate that this thiol-containing motif and its cognate Zn2+ might function as a redox sensor to regulate cell wall synthesis for survival in adverse or anaerobic environments.
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Affiliation(s)
- Michael D Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Shaohui Wang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Swamy R Adapa
- Department of Global and Planetary Health, USF Genomics Program, Global Health and Infectious Disease Center, College of Public Health, University of South Florida, Tampa, FL, 33620, USA
| | - Xiujun Zhang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Eric M Lewandowski
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Maura V Gongora
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | | | - Zachary D Atlas
- School of Geosciences, University of South Florida, Tampa, FL, 33620, USA
| | - Julia A Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Jean R Gatdula
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Ryan T Morgan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Lauren R Hammond
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, AZ, 85721, USA
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Prahathees J Eswara
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Ioannis Gelis
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | - Rays H Y Jiang
- Department of Global and Planetary Health, USF Genomics Program, Global Health and Infectious Disease Center, College of Public Health, University of South Florida, Tampa, FL, 33620, USA
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
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Kong L, Su M, Sang J, Huang S, Wang M, Cai Y, Xie M, Wu J, Wang S, Foster SJ, Zhang J, Han A. The W-Acidic Motif of Histidine Kinase WalK Is Required for Signaling and Transcriptional Regulation in Streptococcus mutans. Front Microbiol 2022; 13:820089. [PMID: 35558126 PMCID: PMC9087282 DOI: 10.3389/fmicb.2022.820089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/14/2022] [Indexed: 02/05/2023] Open
Abstract
In Streptococcus mutans, we find that the histidine kinase WalK possesses the longest C-terminal tail (CTT) among all 14 TCSs, and this tail plays a key role in the interaction of WalK with its response regulator WalR. We demonstrate that the intrinsically disordered CTT is characterized by a conserved tryptophan residue surrounded by acidic amino acids. Mutation in the tryptophan not only disrupts the stable interaction, but also impairs the efficient phosphotransferase and phosphatase activities of WalRK. In addition, the tryptophan is important for WalK to compete with DNA containing a WalR binding motif for the WalR interaction. We further show that the tryptophan is important for in vivo transcriptional regulation and bacterial biofilm formation by S. mutans. Moreover, Staphylococcus aureus WalK also has a characteristic CTT, albeit relatively shorter, with a conserved W-acidic motif, that is required for the WalRK interaction in vitro. Together, these data reveal that the W-acidic motif of WalK is indispensable for its interaction with WalR, thereby playing a key role in the WalRK-dependent signal transduction, transcriptional regulation and biofilm formation.
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Affiliation(s)
- Lingyuan Kong
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mingyang Su
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jiayan Sang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shanshan Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Min Wang
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yongfei Cai
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mingquan Xie
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jun Wu
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shida Wang
- State Key Laboratory for Oral Diseases and National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Simon J Foster
- Department of Molecular Biology and Biotechnology, The Florey Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Jiaqin Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Aidong Han
- State Key Laboratory for Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
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20
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Patel O, Brammananth R, Dai W, Panjikar S, Coppel RL, Lucet IS, Crellin PK. Crystal structure of the putative cell-wall lipoglycan biosynthesis protein LmcA from Mycobacterium smegmatis. Acta Crystallogr D Struct Biol 2022; 78:494-508. [PMID: 35362472 PMCID: PMC8972800 DOI: 10.1107/s2059798322001772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/16/2022] [Indexed: 11/17/2022] Open
Abstract
The first crystal structure of the putative cell-wall biosynthesis protein LmcA from Mycobacterium smegmatis is reported at 1.8 Å resolution. The structure revealed an elongated β-barrel fold enclosing two distinct cavities, indicating a possible lipid-binding function in lipomannan/lipoarabinomannan biosynthesis. The bacterial genus Mycobacterium includes important pathogens, most notably M. tuberculosis, which infects one-quarter of the entire human population, resulting in around 1.4 million deaths from tuberculosis each year. Mycobacteria, and the closely related corynebacteria, synthesize a class of abundant glycolipids, the phosphatidyl-myo-inositol mannosides (PIMs). PIMs serve as membrane anchors for hyperglycosylated species, lipomannan (LM) and lipoarabinomannan (LAM), which are surface-exposed and modulate the host immune response. Previously, in studies using the model species Corynebacterium glutamicum, NCgl2760 was identified as a novel membrane protein that is required for the synthesis of full-length LM and LAM. Here, the first crystal structure of its ortholog in Mycobacterium smegmatis, MSMEG_0317, is reported at 1.8 Å resolution. The structure revealed an elongated β-barrel fold enclosing two distinct cavities and one α-helix extending away from the β-barrel core, resembling a ‘cone with a flake’ arrangement. Through xenon derivatization and structural comparison with AlphaFold2-derived predictions of the M. tuberculosis homolog Rv0227c, structural elements were identified that may undergo conformational changes to switch from ‘closed’ to ‘open’ conformations, allowing cavity access. An AlphaFold2-derived NCgl2760 model predicted a smaller β-barrel core with an enclosed central cavity, suggesting that all three proteins, which were collectively termed LmcA, may have a common mechanism of ligand binding through these cavities. These findings provide new structural insights into the biosynthetic pathway for a family of surface lipoglycans with important roles in mycobacterial pathogenesis.
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21
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Gambelli L, Isupov MN, Conners R, McLaren M, Bellack A, Gold V, Rachel R, Daum B. An archaellum filament composed of two alternating subunits. Nat Commun 2022; 13:710. [PMID: 35132062 PMCID: PMC8821640 DOI: 10.1038/s41467-022-28337-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/20/2022] [Indexed: 02/07/2023] Open
Abstract
Archaea use a molecular machine, called the archaellum, to swim. The archaellum consists of an ATP-powered intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. In many species, several archaellin homologs are encoded in the same operon; however, previous structural studies indicated that archaellum filaments mainly consist of only one protein species. Here, we use electron cryo-microscopy to elucidate the structure of the archaellum from Methanocaldococcus villosus at 3.08 Å resolution. The filament is composed of two alternating archaellins, suggesting that the architecture and assembly of archaella is more complex than previously thought. Moreover, we identify structural elements that may contribute to the filament’s flexibility. The archaellum is a molecular machine used by archaea to swim, consisting of an intracellular motor that drives the rotation of an extracellular filament composed of multiple copies of proteins named archaellins. Here, the authors use electron cryo-microscopy to elucidate the structure of an archaellum, and find that the filament is composed of two alternating archaellins.
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Affiliation(s)
- Lavinia Gambelli
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.,College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, EX4 4QF, UK
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Rebecca Conners
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.,College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.,College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Annett Bellack
- Institute of Microbiology and Archaea Centre, University of Regensburg, 93053, Regensburg, Germany
| | - Vicki Gold
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK.,College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Reinhard Rachel
- Institute of Microbiology and Archaea Centre, University of Regensburg, 93053, Regensburg, Germany
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, EX4 4QD, UK. .,College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK.
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22
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Sandoval K, McCormack GP. Actinoporin-like Proteins Are Widely Distributed in the Phylum Porifera. Mar Drugs 2022; 20:md20010074. [PMID: 35049929 PMCID: PMC8778704 DOI: 10.3390/md20010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 11/16/2022] Open
Abstract
Actinoporins are proteinaceous toxins known for their ability to bind to and create pores in cellular membranes. This quality has generated interest in their potential use as new tools, such as therapeutic immunotoxins. Isolated historically from sea anemones, genes encoding for similar actinoporin-like proteins have since been found in a small number of other animal phyla. Sequencing and de novo assembly of Irish Haliclona transcriptomes indicated that sponges also possess similar genes. An exhaustive analysis of publicly available sequencing data from other sponges showed that this is a potentially widespread feature of the Porifera. While many sponge proteins possess a sequence similarity of 27.70–59.06% to actinoporins, they show consistency in predicted structure. One gene copy from H. indistincta has significant sequence similarity to sea anemone actinoporins and possesses conserved residues associated with the fundamental roles of sphingomyelin recognition, membrane attachment, oligomerization, and pore formation, indicating that it may be an actinoporin. Phylogenetic analyses indicate frequent gene duplication, no distinct clade for sponge-derived proteins, and a stronger signal towards actinoporins than similar proteins from other phyla. Overall, this study provides evidence that a diverse array of Porifera represents a novel source of actinoporin-like proteins which may have biotechnological and pharmaceutical applications.
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23
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Structure of the Streptococcus pyogenes NADase translocation domain and its essential role in toxin binding to oropharyngeal keratinocytes. J Bacteriol 2021; 204:e0036621. [PMID: 34694903 DOI: 10.1128/jb.00366-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The emergence and continued dominance of a Streptococcus pyogenes (group A Streptococcus, GAS) M1T1 clonal group is temporally correlated with acquisition of genomic sequences that confer high level expression of co-toxins streptolysin O (SLO) and NAD+-glycohydrolase (NADase). Experimental infection models have provided evidence that both toxins are important contributors to GAS virulence. SLO is a cholesterol-dependent pore-forming toxin capable of lysing virtually all types of mammalian cells. NADase, which is composed of an N-terminal translocation domain and C-terminal glycohydrolase domain, acts as an intracellular toxin that depletes host cell energy stores. NADase is dependent on SLO for internalization into epithelial cells, but its mechanism of interaction with the cell surface and details of its translocation mechanism remain unclear. In this study we found that NADase can bind oropharyngeal epithelial cells independently of SLO. This interaction is mediated by both domains of the toxin. We determined by NMR the structure of the translocation domain to be a β-sandwich with a disordered N-terminal region. The folded region of the domain has structural homology to carbohydrate binding modules. We show that excess NADase inhibits SLO-mediated hemolysis and binding to epithelial cells in vitro, suggesting NADase and SLO have shared surface receptors. This effect is abrogated by disruption of a putative carbohydrate binding site on the NADase translocation domain. Our data are consistent with a model whereby interactions of the NADase glycohydrolase domain and translocation domain with SLO and the cell surface increase avidity of NADase binding and facilitate toxin-toxin and toxin-cell surface interactions. Importance NADase and streptolysin O (SLO) are secreted toxins important for pathogenesis of group A Streptococcus, the agent of strep throat and severe invasive infections. The two toxins interact in solution and mutually enhance cytotoxic activity. We now find that NADase is capable of binding to the surface of human cells independently of SLO. Structural analysis of the previously uncharacterized translocation domain of NADase suggests that it contains a carbohydrate binding module. The NADase translocation domain and SLO appear to recognize similar glycan structures on the cell surface, which may be one mechanism through which NADase enhances SLO pore-forming activity during infection. Our findings provide new insight into the NADase toxin and its functional interactions with SLO during streptococcal infection.
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24
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Identification and Biochemical Characterization of a Novel Hormone-Sensitive Lipase Family Esterase Est19 from the Antarctic Bacterium Pseudomonas sp. E2-15. Biomolecules 2021; 11:biom11111552. [PMID: 34827549 PMCID: PMC8615396 DOI: 10.3390/biom11111552] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 02/07/2023] Open
Abstract
Esterases represent an important class of enzymes with a wide variety of industrial applications. A novel hormone-sensitive lipase (HSL) family esterase, Est19, from the Antarctic bacterium Pseudomonas sp. E2-15 is identified, cloned, and expressed. The enzyme possesses a GESAG motif containing an active serine (S) located within a highly conserved catalytic triad of Ser155, Asp253, and His282 residues. The catalytic efficiency (kcat/Km) of Est19 for the pNPC6 substrate is 148.68 s-1mM-1 at 40 °C. Replacing Glu154 juxtaposed to the critical catalytic serine with Asp (E154→D substitution) reduced the activity and catalytic efficiency of the enzyme two-fold, with little change in the substrate affinity. The wild-type enzyme retained near complete activity over a temperature range of 10-60 °C, while ~50% of its activity was retained at 0 °C. A phylogenetic analysis suggested that Est19 and its homologs may represent a new subfamily of HSL. The thermal stability and stereo-specificity suggest that the Est19 esterase may be useful for cold and chiral catalyses.
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25
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Proteomic Tools for the Analysis of Cytoskeleton Proteins. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2364:363-425. [PMID: 34542864 DOI: 10.1007/978-1-0716-1661-1_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Proteomic analyses have become an essential part of the toolkit of the molecular biologist, given the widespread availability of genomic data and open source or freely accessible bioinformatics software. Tools are available for detecting homologous sequences, recognizing functional domains, and modeling the three-dimensional structure for any given protein sequence, as well as for predicting interactions with other proteins or macromolecules. Although a wealth of structural and functional information is available for many cytoskeletal proteins, with representatives spanning all of the major subfamilies, the majority of cytoskeletal proteins remain partially or totally uncharacterized. Moreover, bioinformatics tools provide a means for studying the effects of synthetic mutations or naturally occurring variants of these cytoskeletal proteins. This chapter discusses various freely available proteomic analysis tools, with a focus on in silico prediction of protein structure and function. The selected tools are notable for providing an easily accessible interface for the novice while retaining advanced functionality for more experienced computational biologists.
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26
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Sartor P, Denkhaus L, Gerhardt S, Einsle O, Fetzner S. Structural basis of O-methylation of (2-heptyl-)1-hydroxyquinolin-4(1H)-one and related compounds by the heterocyclic toxin methyltransferase Rv0560c of Mycobacterium tuberculosis. J Struct Biol 2021; 213:107794. [PMID: 34506908 DOI: 10.1016/j.jsb.2021.107794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022]
Abstract
The S-adenosyl-L-methionine-dependent methyltransferase Rv0560c of Mycobacterium tuberculosis belongs to an orthologous group of heterocyclic toxin methyltransferases (Htm) which likely contribute to resistance of mycobacteria towards antimicrobial natural compounds as well as drugs. HtmM.t. catalyzes the methylation of the Pseudomonas aeruginosa toxin 2-heptyl-1-hydroxyquinolin-4(1H)-one (also known as 2-heptyl-4-hydroxyquinoline N-oxide), a potent inhibitor of respiratory electron transfer, its 1-hydroxyquinolin-4(1H)-one core (QNO), structurally related (iso)quinolones, and some mycobactericidal compounds. In this study, crystal structures of HtmM.t. in complex with S-adenosyl-L-homocysteine (SAH) and the methyl-accepting substrates QNO or 4-hydroxyisoquinoline-1(2H)-one, or the methylated product 1-methoxyquinolin-4(1H)-one, were determined at < 1.9 Å resolution. The monomeric protein exhibits the typical Rossmann fold topology and conserved residues of class I methyltransferases. Its SAH binding pocket is connected via a short tunnel to a large solvent-accessible cavity, which accommodates the methyl-accepting substrate. Residues W44, F168, and F208 in connection with F212 form a hydrophobic clamp around the heteroaromatic ring of the methyl-accepting substrate and likely play a major role in substrate positioning. Structural and biochemical data suggest that H139 and T136 are key active site residues, with H139 acting as general base that activates the methyl-accepting hydroxy group. Our structural data may contribute to the design of Htm inhibitors or of antimycobacterial drugs unamenable for methylation.
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Affiliation(s)
- Pascal Sartor
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany.
| | - Lukas Denkhaus
- Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany.
| | - Stefan Gerhardt
- Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany.
| | - Oliver Einsle
- Institute for Biochemistry, University of Freiburg, Freiburg im Breisgau, Germany.
| | - Susanne Fetzner
- Institute of Molecular Microbiology and Biotechnology, University of Münster, Münster, Germany.
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27
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Marjanovic A, Rozeboom HJ, de Vries MS, Mayer C, Otzen M, Wijma HJ, Janssen DB. Catalytic and structural properties of ATP-dependent caprolactamase from Pseudomonas jessenii. Proteins 2021; 89:1079-1098. [PMID: 33826169 PMCID: PMC8453981 DOI: 10.1002/prot.26082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/04/2021] [Accepted: 03/22/2021] [Indexed: 12/14/2022]
Abstract
Caprolactamase is the first enzyme in the caprolactam degradation pathway of Pseudomonas jessenii. It is composed of two subunits (CapA and CapB) and sequence-related to other ATP-dependent enzymes involved in lactam hydrolysis, like 5-oxoprolinases and hydantoinases. Low sequence similarity also exists with ATP-dependent acetone- and acetophenone carboxylases. The caprolactamase was produced in Escherichia coli, isolated by His-tag affinity chromatography, and subjected to functional and structural studies. Activity toward caprolactam required ATP and was dependent on the presence of bicarbonate in the assay buffer. The hydrolysis product was identified as 6-aminocaproic acid. Quantum mechanical modeling indicated that the hydrolysis of caprolactam was highly disfavored (ΔG0 '= 23 kJ/mol), which explained the ATP dependence. A crystal structure showed that the enzyme exists as an (αβ)2 tetramer and revealed an ATP-binding site in CapA and a Zn-coordinating site in CapB. Mutations in the ATP-binding site of CapA (D11A and D295A) significantly reduced product formation. Mutants with substitutions in the metal binding site of CapB (D41A, H99A, D101A, and H124A) were inactive and less thermostable than the wild-type enzyme. These residues proved to be essential for activity and on basis of the experimental findings we propose possible mechanisms for ATP-dependent lactam hydrolysis.
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Affiliation(s)
- Antonija Marjanovic
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | - Henriëtte J. Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | - Meintje S. de Vries
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | - Clemens Mayer
- Biomolecular Chemistry and Catalysis, Stratingh Institute for ChemistryUniversity of GroningenGroningenThe Netherlands
| | - Marleen Otzen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | | | - Dick B. Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
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28
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Penev PI, McCann HM, Meade CD, Alvarez-Carreño C, Maddala A, Bernier CR, Chivukula VL, Ahmad M, Gulen B, Sharma A, Williams LD, Petrov AS. ProteoVision: web server for advanced visualization of ribosomal proteins. Nucleic Acids Res 2021; 49:W578-W588. [PMID: 33999189 PMCID: PMC8265156 DOI: 10.1093/nar/gkab351] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/11/2021] [Accepted: 04/21/2021] [Indexed: 11/26/2022] Open
Abstract
ProteoVision is a web server designed to explore protein structure and evolution through simultaneous visualization of multiple sequence alignments, topology diagrams and 3D structures. Starting with a multiple sequence alignment, ProteoVision computes conservation scores and a variety of physicochemical properties and simultaneously maps and visualizes alignments and other data on multiple levels of representation. The web server calculates and displays frequencies of amino acids. ProteoVision is optimized for ribosomal proteins but is applicable to analysis of any protein. ProteoVision handles internally generated and user uploaded alignments and connects them with a selected structure, found in the PDB or uploaded by the user. It can generate de novo topology diagrams from three-dimensional structures. All displayed data is interactive and can be saved in various formats as publication quality images or external datasets or PyMol Scripts. ProteoVision enables detailed study of protein fragments defined by Evolutionary Classification of protein Domains (ECOD) classification. ProteoVision is available at http://proteovision.chemistry.gatech.edu/.
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Affiliation(s)
- Petar I Penev
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Holly M McCann
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Caeden D Meade
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Claudia Alvarez-Carreño
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Aparna Maddala
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Chad R Bernier
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Vasanta L Chivukula
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Maria Ahmad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Burak Gulen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Aakash Sharma
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Loren Dean Williams
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Anton S Petrov
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
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29
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Sadeghian I, Hemmati S. Characterization of a Stable Form of Carboxypeptidase G2 (Glucarpidase), a Potential Biobetter Variant, From Acinetobacter sp. 263903-1. Mol Biotechnol 2021; 63:1155-1168. [PMID: 34268672 DOI: 10.1007/s12033-021-00370-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/08/2021] [Indexed: 01/14/2023]
Abstract
Carboxypeptidase G2 (CPG2) is a bacterial enzyme widely used to detoxify methotrexate (MTX) and in enzyme/prodrug therapy for cancer treatment. However, several drawbacks, such as instability, have limited its efficiency. Herein, we have evaluated the properties of a putative CPG2 from Acinetobacter sp. 263903-1 (AcCPG2). AcCPG2 is compared with a CPG2 derived from Pseudomonas sp. strain RS-16 (PsCPG2), available as an FDA-approved medication called glucarpidase. After modeling AcCPG2 using the I-TASSER program, the refined model was validated by PROCHECK, VERIFY 3D and according to the Z score of the model. Using computational analyses, AcCPG2 displayed higher thermodynamic stability and a lower aggregation propensity than PsCPG2. AcCPG2 showed an optimum pH of 7.5 against MTX and was stable over a pH range of 5-10. AcCPG2 exhibited optimum activity at 50 °C and higher thermal stability at a temperature range of 20-70 °C compared to PsCPG2. The Km value of the purified AcCPG2 toward folate and MTX was 31.36 µM and 44.99 µM, respectively. The Vmax value of AcCPG2 for folate and MTX was 125.80 µmol/min/mg and 48.90 µmol/min/mg, respectively. Accordingly, thermostability and pH versatility makes AcCPG2 a potential biobetter variant for therapeutic applications.
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Affiliation(s)
- Issa Sadeghian
- Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shiva Hemmati
- Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
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30
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Hutařová Vařeková I, Hutař J, Midlik A, Horský V, Hladká E, Svobodová R, Berka K. 2DProts: Database of Family-Wide Protein Secondary Structure Diagrams. Bioinformatics 2021; 37:4599-4601. [PMID: 34244700 PMCID: PMC8652034 DOI: 10.1093/bioinformatics/btab505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/28/2021] [Accepted: 07/05/2021] [Indexed: 11/15/2022] Open
Abstract
Summary Secondary structures provide a deep insight into the protein architecture. They can serve for comparison between individual protein family members. The most straightforward way how to deal with protein secondary structure is its visualization using 2D diagrams. Several software tools for the generation of 2D diagrams were developed. Unfortunately, they create 2D diagrams based on only a single protein. Therefore, 2D diagrams of two proteins from one family markedly differ. For this reason, we developed the 2DProts database, which contains secondary structure 2D diagrams for all domains from the CATH and all proteins from PDB databases. These 2D diagrams are generated based on a whole protein family, and they also consider information about the 3D arrangement of secondary structure elements. Moreover, 2DProts database contains multiple 2D diagrams, which provide an overview of a whole protein family's secondary structures. 2DProts is updated weekly and is integrated into CATH. Availability and Implementation Freely accessible at https://2dprots.ncbr.muni.cz. The web interface was implemented in JavaScript. The database was implemented in Python. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ivana Hutařová Vařeková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic.,CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic.,Faculty of Informatics, Masaryk University, Brno, 602 00, Czech Republic
| | - Jan Hutař
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic.,CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Adam Midlik
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic.,CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Vladimír Horský
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic.,CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Eva Hladká
- Faculty of Informatics, Masaryk University, Brno, 602 00, Czech Republic
| | - Radka Svobodová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic.,CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Karel Berka
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Olomouc, 771 46, Czech Republic
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31
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Yuan T, Werman JM, Yin X, Yang M, Garcia-Diaz M, Sampson NS. Enzymatic β-Oxidation of the Cholesterol Side Chain in Mycobacterium tuberculosis Bifurcates Stereospecifically at Hydration of 3-Oxo-cholest-4,22-dien-24-oyl-CoA. ACS Infect Dis 2021; 7:1739-1751. [PMID: 33826843 PMCID: PMC8204306 DOI: 10.1021/acsinfecdis.1c00069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
The unique ability
of Mycobacterium tuberculosis (Mtb) to utilize host
lipids such as cholesterol for survival, persistence,
and virulence has made the metabolic pathway of cholesterol an area
of great interest for therapeutics development. Herein, we identify
and characterize two genes from the Cho-region (genomic locus responsible
for cholesterol catabolism) of the Mtb genome, chsH3 (Rv3538) and chsB1 (Rv3502c). Their protein products
catalyze two sequential stereospecific hydration and dehydrogenation
steps in the β-oxidation of the cholesterol side chain. ChsH3
favors the 22S hydration of 3-oxo-cholest-4,22-dien-24-oyl-CoA
in contrast to the previously reported EchA19 (Rv3516), which catalyzes
formation of the (22R)-hydroxy-3-oxo-cholest-4-en-24-oyl-CoA
from the same enoyl-CoA substrate. ChsB1 is stereospecific and catalyzes
dehydrogenation of the ChsH3 product but not the EchA19 product. The
X-ray crystallographic structure of the ChsB1 apo-protein was determined
at a resolution of 2.03 Å, and the holo-enzyme with bound NAD+ cofactor was determined at a resolution of 2.21 Å. The
homodimeric structure is representative of a classical NAD+-utilizing short-chain type alcohol dehydrogenase/reductase, including
a Rossmann-fold motif, but exhibits a unique substrate binding site
architecture that is of greater length and width than its homologous
counterparts, likely to accommodate the bulky steroid substrate. Intriguingly,
Mtb utilizes hydratases from the MaoC-like family in sterol side-chain
catabolism in contrast to fatty acid β-oxidation in other species
that utilize the evolutionarily distinct crotonase family of hydratases.
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Affiliation(s)
- Tianao Yuan
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Joshua M. Werman
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Xingyu Yin
- Biochemistry and Structural Biology Graduate Program, Stony Brook University, Stony Brook, New York 11794-5215, United States
| | - Meng Yang
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Miguel Garcia-Diaz
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-8651, United States
| | - Nicole S. Sampson
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
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32
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Wolf JN, Keßler M, Ackermann J, Koch I. PTGL: extension to graph-based topologies of cryo-EM data for large protein structures. Bioinformatics 2021; 37:1032-1034. [PMID: 32780800 DOI: 10.1093/bioinformatics/btaa706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/16/2020] [Accepted: 07/30/2020] [Indexed: 11/12/2022] Open
Abstract
SUMMARY We provide a software to describe the topology of large protein complexes based mainly on cryo-EM data and stored as macromolecular Crystallographic Information Files (mmCIFs) in the PDB. The software extends the Protein Topology Graph Library and implements an efficient file parser to analyze mmCIFs. The extended Protein Topology Graph Library includes a graph-based representation of the topology of protein complexes on the supersecondary and quaternary structure level. The library holds topology graphs of 151 837 PDB files; 921 of them are large structures. The abstraction of protein structure complexes to undirected labeled graphs enables classification and comparison of large protein complexes on quaternary structure level. AVAILABILITY AND IMPLEMENTATION Online access at http://ptgl.uni-frankfurt.de. Source code in Java under GNU public license 2.0 at https://github.com/MolBIFFM/vplg. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jan Niclas Wolf
- Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, Johann Wolfgang Goethe-University Frankfurt am Main, 60325 Frankfurt am Main, Germany
| | - Marcus Keßler
- Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, Johann Wolfgang Goethe-University Frankfurt am Main, 60325 Frankfurt am Main, Germany
| | - Jörg Ackermann
- Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, Johann Wolfgang Goethe-University Frankfurt am Main, 60325 Frankfurt am Main, Germany
| | - Ina Koch
- Molecular Bioinformatics, Institute of Computer Science, Faculty of Computer Science and Mathematics, Johann Wolfgang Goethe-University Frankfurt am Main, 60325 Frankfurt am Main, Germany
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Dijkman PM, Marzluf T, Zhang Y, Chang SYS, Helm D, Lanzer M, Bujard H, Kudryashev M. Structure of the merozoite surface protein 1 from Plasmodium falciparum. SCIENCE ADVANCES 2021; 7:7/23/eabg0465. [PMID: 34078606 DOI: 10.1126/sciadv.abg0465] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/14/2021] [Indexed: 06/12/2023]
Abstract
The merozoite surface protein 1 (MSP-1) is the most abundant protein on the surface of the erythrocyte-invading Plasmodium merozoite, the causative agent of malaria. MSP-1 is essential for merozoite formation, entry into and escape from erythrocytes, and is a promising vaccine candidate. Here, we present monomeric and dimeric structures of full-length MSP-1. MSP-1 adopts an unusual fold with a large central cavity. Its fold includes several coiled-coils and shows structural homology to proteins associated with membrane and cytoskeleton interactions. MSP-1 formed dimers through these domains in a concentration-dependent manner. Dimerization is affected by the presence of the erythrocyte cytoskeleton protein spectrin, which may compete for the dimerization interface. Our work provides structural insights into the possible mode of interaction of MSP-1 with erythrocytes and establishes a framework for future investigations into the role of MSP-1 in Plasmodium infection and immunity.
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Affiliation(s)
- Patricia M Dijkman
- Max-Planck-Institute of Biophysics, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University of Frankfurt, Frankfurt am Main, Germany
| | - Tanja Marzluf
- Centre for Infectious Diseases, Parasitology Unit, Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany
- MS-based Protein Analysis Unit, Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yingyi Zhang
- Max-Planck-Institute of Biophysics, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University of Frankfurt, Frankfurt am Main, Germany
| | - Shih-Ying Scott Chang
- Max-Planck-Institute of Biophysics, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University of Frankfurt, Frankfurt am Main, Germany
| | - Dominic Helm
- MS-based Protein Analysis Unit, Genomics and Proteomics Core Facility, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Lanzer
- Centre for Infectious Diseases, Parasitology Unit, Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany
| | - Hermann Bujard
- Sumaya Biotech GmbH & Co. KG, Heidelberg, Germany
- Centre for Molecular Biology Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Mikhail Kudryashev
- Max-Planck-Institute of Biophysics, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University of Frankfurt, Frankfurt am Main, Germany
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Padavattan S, Jos S, Gogoi H, Bagautdinov B. Crystal structure of enoyl-CoA hydratase from Thermus thermophilus HB8. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2021; 77:148-155. [PMID: 33949975 DOI: 10.1107/s2053230x21004593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/30/2021] [Indexed: 11/11/2022]
Abstract
Fatty-acid degradation is an oxidative process that involves four enzymatic steps and is referred to as the β-oxidation pathway. During this process, long-chain acyl-CoAs are broken down into acetyl-CoA, which enters the mitochondrial tricarboxylic acid (TCA) cycle, resulting in the production of energy in the form of ATP. Enoyl-CoA hydratase (ECH) catalyzes the second step of the β-oxidation pathway by the syn addition of water to the double bond between C2 and C3 of a 2-trans-enoyl-CoA, resulting in the formation of a 3-hydroxyacyl CoA. Here, the crystal structure of ECH from Thermus thermophilus HB8 (TtECH) is reported at 2.85 Å resolution. TtECH forms a hexamer as a dimer of trimers, and wide clefts are uniquely formed between the two trimers. Although the overall structure of TtECH is similar to that of a hexameric ECH from Rattus norvegicus (RnECH), there is a significant shift in the positions of the helices and loops around the active-site region, which includes the replacement of a longer α3 helix with a shorter α-helix and 310-helix in RnECH. Additionally, one of the catalytic residues of RnECH, Glu144 (numbering based on the RnECH enzyme), is replaced by a glycine in TtECH, while the other catalytic residue Glu164, as well as Ala98 and Gly141 that stabilize the enolate intermediate, is conserved. Their putative ligand-binding sites and active-site residue compositions are dissimilar.
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Affiliation(s)
- Sivaraman Padavattan
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore 560 029, India
| | - Sneha Jos
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore 560 029, India
| | - Hemanga Gogoi
- Department of Biophysics, National Institute of Mental Health and Neurosciences, Bangalore 560 029, India
| | - Bagautdin Bagautdinov
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
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Zegarra FC, Homouz D, Wittung-Stafshede P, Cheung MS. The Zero-Order Loop in Apoazurin Modulates Folding Mechanism In Silico. J Phys Chem B 2021; 125:3501-3509. [PMID: 33818090 DOI: 10.1021/acs.jpcb.1c00219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Pseudomonas aeruginosa apoazurin (apo, without the copper cofactor) has a single disulfide bond between residues 3 and 26 and unfolds in a two-state reaction in vitro. The disulfide bond covalently connects the N-termini of β-strands 1 and 3; thereby, it creates a zero-order loop or a "cinch" that restricts conformational space. Covalent loops and threaded topologies are emerging as important structural elements in folded proteins and may be important for function. In order to understand the role of a zero-order loop in the folding process of a protein, here we used coarse-grained molecular dynamics (CGMD) simulations in silico to compare two variants of apoazurin: one named "loop" which contained the disulfide, and another named "open" in which the disulfide bond between residues 3 and 26 was removed. CGMD simulations were performed to probe the stability and unfolding pathway of the two apoazurin variants at different urea concentrations and temperatures. Our results show that the covalent loop plays a prominent role in the unfolding mechanism of apoazurin; its removal alters both the folding-transition state and the unfolded-state ensemble of conformations. We propose that modulation of azurin's folding landscape by the disulfide bridge may be related to both copper capturing and redox sensing.
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Affiliation(s)
- Fabio C Zegarra
- Laboratorio de Sistemas Inteligentes, EPIME, Universidad Nacional Tecnológica de Lima Sur (UNTELS), Lima 15834, Peru.,Department of Physics, University of Houston, Houston, Texas 77204, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Dirar Homouz
- Department of Physics, Khalifa University of Science and Technology, P.O. Box 127788, Abu Dhabi, 127788 United Arab Emirates.,Department of Physics, University of Houston, Houston, Texas 77204, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
| | - Pernilla Wittung-Stafshede
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Margaret S Cheung
- Pacific Northwest National Laboratory, Research Science Center, Seattle, Washington 98109, United States.,Department of Physics, University of Washington, Seattle, Washington 98195, United States.,Department of Physics, University of Houston, Houston, Texas 77204, United States.,Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, United States
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Hauge Pedersen M, Pham J, Mancebo H, Inoue A, Asher WB, Javitch JA. A novel luminescence-based β-arrestin recruitment assay for unmodified receptors. J Biol Chem 2021; 296:100503. [PMID: 33684444 PMCID: PMC8027564 DOI: 10.1016/j.jbc.2021.100503] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 03/02/2021] [Indexed: 01/14/2023] Open
Abstract
G protein-coupled receptors (GPCRs) signal through activation of G proteins and subsequent modulation of downstream effectors. More recently, signaling mediated by β-arrestin has also been implicated in important physiological functions. This has led to great interest in the identification of biased ligands that favor either G protein or β-arrestin-signaling pathways. However, nearly all screening techniques for measuring β-arrestin recruitment have required C-terminal receptor modifications that can in principle alter protein interactions and thus signaling. Here, we have developed a novel luminescence-based assay to measure β-arrestin recruitment to the membrane or early endosomes by unmodified receptors. Our strategy uses NanoLuc, an engineered luciferase from Oplophorus gracilirostris (deep-sea shrimp) that is smaller and brighter than other well-established luciferases. Recently, several publications have explored functional NanoLuc split sites for use in complementation assays. We have identified a unique split site within NanoLuc and fused the corresponding N-terminal fragment to either a plasma membrane or early endosome tether and the C-terminal fragment to β-arrestins, which form the basis for the MeNArC and EeNArC assays, respectively. Upon receptor activation, β-arrestin is recruited to the membrane and subsequently internalized in an agonist concentration-dependent manner. This recruitment promotes complementation of the two NanoLuc fragments, thereby reconstituting functional NanoLuc, allowing for quantification of β-arrestin recruitment with a single luminescence signal. Our assay avoids potential artifacts related to C-terminal receptor modification and has promise as a new generic assay for measuring β-arrestin recruitment to diverse GPCR types in heterologous or native cells.
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Affiliation(s)
- Maria Hauge Pedersen
- Departments of Psychiatry & Molecular Pharmacology and Therapeutics, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York, USA; NNF Center for Basic Metabolic Research, Section for Metabolic Receptology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | | | - Asuka Inoue
- Department of Pharmacological Sciences, Tohoku University, Sendai, Japan
| | - Wesley B Asher
- Departments of Psychiatry & Molecular Pharmacology and Therapeutics, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York, USA
| | - Jonathan A Javitch
- Departments of Psychiatry & Molecular Pharmacology and Therapeutics, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York, USA.
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37
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Three-dimensional structure of human cyclooxygenase (hCOX)-1. Sci Rep 2021; 11:4312. [PMID: 33619313 PMCID: PMC7900114 DOI: 10.1038/s41598-021-83438-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 02/02/2021] [Indexed: 12/11/2022] Open
Abstract
The beneficial effects of Cyclooxygenases (COX) inhibitors on human health have been known for thousands of years. Nevertheless, COXs, particularly COX-1, have been linked to a plethora of human diseases such as cancer, heart failure, neurological and neurodegenerative diseases only recently. COXs catalyze the first step in the biosynthesis of prostaglandins (PGs) and are among the most important mediators of inflammation. All published structural work on COX-1 deals with the ovine isoenzyme, which is easier to produce in milligram-quantities than the human enzyme and crystallizes readily. Here, we report the long-sought structure of the human cyclooxygenase-1 (hCOX-1) that we refined to an R/Rfree of 20.82/26.37, at 3.36 Å resolution. hCOX-1 structure provides a detailed picture of the enzyme active site and the residues crucial for inhibitor/substrate binding and catalytic activity. We compared hCOX-1 crystal structure with the ovine COX-1 and human COX-2 structures by using metrics based on Cartesian coordinates, backbone dihedral angles, and solvent accessibility coupled with multivariate methods. Differences and similarities among structures are discussed, with emphasis on the motifs responsible for the diversification of the various enzymes (primary structure, stability, catalytic activity, and specificity). The structure of hCOX-1 represents an essential step towards the development of new and more selective COX-1 inhibitors of enhanced therapeutic potential.
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38
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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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Azulay H, Pellach Leshem M, Qvit N. An Approach to comparing protein structures and origami models - Part 2. Multi-domain proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183411. [PMID: 32710853 DOI: 10.1016/j.bbamem.2020.183411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 11/29/2022]
Abstract
Protein structure is an important field of research, with particular significance in its potential applications in biomedicine and nanotechnology. In a recent study, we presented a general approach for comparing protein structures and origami models and demonstrated it with single-domain proteins. For example, the analysis of the α-helical barrel of the outer membrane protein A (OmpA) suggests that there are similar patterns between its structure and the Kresling origami model, providing insight into structure-activity relationships. Here we demonstrate that our approach can be expanded beyond single-domain proteins to also include multi-domain proteins, and to study dynamic processes of biomolecules. Two examples are given: (1) The eukaryotic chaperonin (TRiC) protein is compared with a newly generated origami model, and with an origami model that is constructed from two copies of the Flasher origami model, and (2) the CorA Magnesium transport system is compared with a newly generated origami model and with an origami model that combines the Kresling and Flasher origami models. Based on the analysis of the analog origami models, it is indicated that it is possible to identify building blocks for constructing assembled origami models that are analogous to protein structures. In addition, it is identified that the expansion/collapse mechanisms of the TRiC and CorA are auxetic. Namely, these proteins require a single motion for synchronized folding along two or three axes.
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Affiliation(s)
| | - Michal Pellach Leshem
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, POB 1589, Safed, Israel
| | - Nir Qvit
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, POB 1589, Safed, Israel.
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40
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Goh BC, Chua YK, Qian X, Lin J, Savko M, Dedon PC, Lescar J. Crystal structure of the periplasmic sensor domain of histidine kinase VbrK suggests indirect sensing of β-lactam antibiotics. J Struct Biol 2020; 212:107610. [DOI: 10.1016/j.jsb.2020.107610] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 11/25/2022]
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Yang J, Guan X, Zhang D, Zhao P, Guo S, Kuang Z. Crystal structure of the SPRY domain-containing protein 7 reveals unique structural features. Biochem Biophys Res Commun 2020; 531:350-356. [PMID: 32800543 DOI: 10.1016/j.bbrc.2020.07.076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022]
Abstract
The SPRY/B30.2 domain is one of the most abundant protein domains found in eukaryotes. Vast majority of the SPRY domain-containing proteins are multi-domain proteins. The SPRY domain-containing protein 7 (SPRY7, also named C13orf1, and named chronic lymphocytic leukemia deletion region gene 6 protein, CCLD6, encoded by the spryd7 gene) is the smallest SPRY domain protein in human that does not contain other accessory domains. Here we have determined the crystal structure of human SPRY7 at a resolution of 1.62 Å and found that SPRY7 has some unique structural features that are not present in other previously reported SRPY domain structures. Overall, SPRY7 may represent an evolutionary early version of the SPRY domain, and subsequent loop insertions and expansions, residue substitutions, as well as domain combinations have rendered the SPRY domain versatile binding specificities and broad biological functions. These results serve as a useful basis for a profound characterization of the molecular interactions of SPRY7.
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Affiliation(s)
- Jinjin Yang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Xueyan Guan
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Danting Zhang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Panqi Zhao
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Shujun Guo
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China
| | - Zhihe Kuang
- Department of Cell Biology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China; Institute of Biomedicine, Jinan University, Guangzhou, 510632, China; Guangdong Provincial Key Laboratory of Bioengineering Medicine, Guangzhou, 510632, China.
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42
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Midgett CR, Swindell RA, Pellegrini M, Jon Kull F. A disulfide constrains the ToxR periplasmic domain structure, altering its interactions with ToxS and bile-salts. Sci Rep 2020; 10:9002. [PMID: 32488093 PMCID: PMC7265457 DOI: 10.1038/s41598-020-66050-5] [Citation(s) in RCA: 5] [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: 02/17/2020] [Accepted: 05/13/2020] [Indexed: 11/10/2022] Open
Abstract
ToxR is a transmembrane transcription factor that, together with its integral membrane periplasmic binding partner ToxS, is conserved across the Vibrionaceae family. In some pathogenic Vibrios, including V. parahaemolyticus and V. cholerae, ToxR is required for bile resistance and virulence, and ToxR is fully activated and protected from degradation by ToxS. ToxS achieves this in part by ensuring formation of an intra-chain disulfide bond in the C-terminal periplasmic domain of ToxR (dbToxRp). In this study, biochemical analysis showed dbToxRp to have a higher affinity for the ToxS periplasmic domain than the non-disulfide bonded conformation. Analysis of our dbToxRp crystal structure showed this is due to disulfide bond stabilization. Furthermore, dbToxRp is structurally homologous to the V. parahaemolyticus VtrA periplasmic domain. These results highlight the critical structural role of disulfide bond in ToxR and along with VtrA define a domain fold involved in environmental sensing conserved across the Vibrionaceae family.
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Affiliation(s)
| | | | | | - F Jon Kull
- Department of Chemistry, Dartmouth College, Hanover, NH, USA
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Abstract
The Ca2+-dependent clip-and-link activity of large repeat-in-toxin (RTX) proteins is an exceptional posttranslational process in which an internal domain called a self-processing module (SPM) mediates Ca2+-dependent processing of a highly specific aspartate-proline (Asp-Pro) peptide bond and covalent linkage of the released aspartyl to an adjacent lysine residue through an isopeptide bond. Here, we report the solution structures of the Ca2+-loaded SPM (Ca-SPM) defining the mechanism of the autocatalytic cleavage of the Asp414-Pro415 peptide bond of the Neisseria meningitidis FrpC exoprotein. Moreover, deletion of the SPM domain in the ApxIVA protein, the FrpC homolog of Actinobacillus pleuropneumoniae, resulted in attenuation of virulence of the bacterium in a pig infection model, indicating that the Ca2+-dependent clip-and-link activity plays a role in the virulence of Gram-negative pathogens. The posttranslational Ca2+-dependent “clip-and-link” activity of large repeat-in-toxin (RTX) proteins starts by Ca2+-dependent structural rearrangement of a highly conserved self-processing module (SPM). Subsequently, an internal aspartate-proline (Asp-Pro) peptide bond at the N-terminal end of SPM breaks, and the liberated C-terminal aspartyl residue can react with a free ε-amino group of an adjacent lysine residue to form a new isopeptide bond. Here, we report a solution structure of the calcium-loaded SPM (Ca-SPM) derived from the FrpC protein of Neisseria meningitidis. The Ca-SPM structure defines a unique protein architecture and provides structural insight into the autocatalytic cleavage of the Asp-Pro peptide bond through a “twisted-amide” activation. Furthermore, in-frame deletion of the SPM domain from the ApxIVA protein of Actinobacillus pleuropneumoniae attenuated the virulence of this porcine pathogen in a pig respiratory challenge model. We hypothesize that the Ca2+-dependent clip-and-link activity represents an unconventional strategy for Gram-negative pathogens to adhere to the host target cell surface.
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Muthuvel Prasath K, Ganesan K, Parthasarathy S. PredictSuperFam-PSS-3D1D: A server for predicting superfamily for the annotation of twilight zone protein sequences. J Struct Biol 2020; 210:107479. [PMID: 32081792 DOI: 10.1016/j.jsb.2020.107479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 12/25/2019] [Accepted: 02/14/2020] [Indexed: 10/25/2022]
Abstract
Annotation of twilight zone protein sequences has been hitherto attempted by predicting the fold of the given sequence. We report here the PredictSuperFam-PSS-3D1D method, which predicts the superfamily for a given twilight zone (TZ) protein sequence. Earlier, we have reported that adding predicted secondary structure information into the threading methods could improve fold prediction especially for the TZ protein sequences. In this study, we have analysed the application of the same method to predict superfamilies. Here, in this method, the twilight zone protein sequence is threaded with the 3D1D profiles of the known protein superfamilies library. In addition, weightage for the predicted secondary structure (PSS) is also employed. The performance of the method is benchmarked with twilight zone sequences. In the benchmarks, 62 and 65 percentages of superfamily predictions are obtained with GOR IV and NPS@ predicted secondary structures, respectively. Receiver Operating Characteristic (ROC) curves indicate that the method is sensitive in predicting the superfamilies. A case study has been conducted with the hypothetical protein sequences of Schistosoma haematobium (Blood Fluke) using this method and the results are analyzed. Our method predicts the superfamily for TZ sequences for which, methods based on sequence similarity alone are inadequate. A web server has been developed for our method and it is available online at http://bioinfo.bdu.ac.in/psfpss.
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Affiliation(s)
- K Muthuvel Prasath
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
| | - K Ganesan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, Tamil Nadu, India
| | - S Parthasarathy
- Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India.
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45
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Azulay H, Lutaty A, Qvit N. Approach for comparing protein structures and origami models. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183132. [PMID: 31738904 DOI: 10.1016/j.bbamem.2019.183132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/05/2019] [Accepted: 10/28/2019] [Indexed: 11/20/2022]
Abstract
The research fields of proteins and origami have intersected in the study of folding and de-novo design of proteins. However, there is limited knowledge on the analogy between protein structures and origami models. We propose a general approach for comparing protein structures with origami models, and present a test case, comparing transmembrane β-barrel and α-helical barrel with the Yoshimura and Kresling origami models. While both shapes and structures may look similar, we demonstrated that the β-barrel and the α-helical barrel are in agreement only with the shape and structural characteristics of the Kresling model. Through the analogy, it is explained how the structural characteristic can help the β-barrel and α-helical barrel to adjust length and diameter in response to changes in the membrane structure. However, such conformations only apply to the α-helical barrel, and the β-barrel, in spite of resembles to the Kresling model, remains stiff due to hydrogen bonds between the β-strands. Thus, our analysis suggests that there are similar patterns between protein structures and origami models and that the proposed approach may provide important insight on the role that the structure of a protein fulfils, and on the preferred structural design of novel proteins with unique characteristics.
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Affiliation(s)
| | | | - Nir Qvit
- The Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, POB 1589, Safed, Israel.
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Zhang L, Zhu L, Qu W, Wu F, Hu M, Xie W, Liu Z, Wang C. Insight into tartrate inhibition patterns in vitro and in vivo based on cocrystal structure with UDP-glucuronosyltransferase 2B15. Biochem Pharmacol 2020; 172:113753. [DOI: 10.1016/j.bcp.2019.113753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/10/2019] [Indexed: 01/08/2023]
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Latham RD, Torrado M, Atto B, Walshe JL, Wilson R, Guss JM, Mackay JP, Tristram S, Gell DA. A heme-binding protein produced by Haemophilus haemolyticus inhibits non-typeable Haemophilus influenzae. Mol Microbiol 2019; 113:381-398. [PMID: 31742788 DOI: 10.1111/mmi.14426] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 01/02/2023]
Abstract
Commensal bacteria serve as an important line of defense against colonisation by opportunisitic pathogens, but the underlying molecular mechanisms remain poorly explored. Here, we show that strains of a commensal bacterium, Haemophilus haemolyticus, make hemophilin, a heme-binding protein that inhibits growth of the opportunistic pathogen, non-typeable Haemophilus influenzae (NTHi) in culture. We purified the NTHi-inhibitory protein from H. haemolyticus and identified the hemophilin gene using proteomics and a gene knockout. An x-ray crystal structure of recombinant hemophilin shows that the protein does not belong to any of the known heme-binding protein folds, suggesting that it evolved independently. Biochemical characterisation shows that heme can be captured in the ferrous or ferric state, and with a variety of small heme-ligands bound, suggesting that hemophilin could function under a range of physiological conditions. Hemophilin knockout bacteria show a limited capacity to utilise free heme for growth. Our data suggest that hemophilin is a hemophore and that inhibition of NTHi occurs by heme starvation, raising the possibility that competition from hemophilin-producing H. haemolyticus could antagonise NTHi colonisation in the respiratory tract.
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Affiliation(s)
- Roger D Latham
- School of Medicine, University of Tasmania, Hobart, Australia
| | - Mario Torrado
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Brianna Atto
- School of Health Sciences, University of Tasmania, Launceston, Australia
| | - James L Walshe
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, Australia
| | - J Mitchell Guss
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | - Stephen Tristram
- School of Health Sciences, University of Tasmania, Launceston, Australia
| | - David A Gell
- School of Medicine, University of Tasmania, Hobart, Australia
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48
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Been KW, Yoon HJ, Jeon ST, Lee HH. Structural characterization of a putative diguanylate cyclase conserved in hyperthermophiles. Biochem Biophys Res Commun 2019; 518:114-119. [PMID: 31420168 DOI: 10.1016/j.bbrc.2019.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 10/26/2022]
Abstract
C-di-GMP, bis-(3'-5')-cyclic dimeric guanosine monophosphate, is a key signaling molecule that regulates many important physiological processes in bacteria. C-di-GMP is synthesized by diguanylate cyclase (DGC) containing the homodimeric GGDEF domain. There are many uncharacterized hypothetical proteins annotated as a putative DGC in bacteria including hyperthermophiles; however, their structures still remain unexplored. Here, we solved the crystal structure of the GGDEF-like domain of Tm0107 protein from Thermotoga maritima at a resolution of 2.1 Å, which shares sequence similarities with DGC proteins in other bacteria. Tm0107 consists of an N-terminal coiled-coil and C-terminal GGDEF-like domain. We showed that the GGDEF-like domain of Tm0107 exists as monomer in solution and is structurally similar to other GGDEF domains. Two zinc ions are coordinated at the interface between two Tm0107 monomers. Based on our measurements of the Stokes radii of Tm0107 by analytical gel filtration, we propose a dimer model of Tm0107 containing both the N-terminal coiled coil and C-terminal GGDEF-like domains. Based on the model, Tm0107 forms a homodimer in a manner different compared to other structurally characterized DGC proteins. These results provide useful structural information about putative DGC proteins containing protein sequences similar to that of Tm0107, which is widely conserved in hyperthermophiles.
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Affiliation(s)
- Kyung Wook Been
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seung Taeg Jeon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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49
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Bauer KM, Dicovitsky R, Pellegrini M, Zhaxybayeva O, Ragusa MJ. The structure of a highly-conserved picocyanobacterial protein reveals a Tudor domain with an RNA-binding function. J Biol Chem 2019; 294:14333-14344. [PMID: 31391250 DOI: 10.1074/jbc.ra119.007938] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 08/06/2019] [Indexed: 11/06/2022] Open
Abstract
Cyanobacteria of the Prochlorococcus and marine Synechococcus genera are the most abundant photosynthetic microbes in the ocean. Intriguingly, the genomes of these bacteria are strongly divergent even within each genus, both in gene content and at the amino acid level of the encoded proteins. One striking exception to this is a 62-amino-acid protein, termed Prochlorococcus/ Synechococcus hyper-conserved protein (PSHCP). PSHCP is not only found in all sequenced Prochlorococcus and marine Synechococcus genomes, but it is also nearly 100% identical in its amino acid sequence across all sampled genomes. Such universal distribution and sequence conservation suggest an essential cellular role of PSHCP in these bacteria. However, its function is unknown. Here, we used NMR spectroscopy to determine its structure, finding that 53 of the 62 amino acids in PSHCP form a Tudor domain, whereas the remainder of the protein is disordered. NMR titration experiments revealed that PSHCP has only a weak affinity for DNA, but an 18.5-fold higher affinity for tRNA, hinting at an involvement of PSHCP in translation. Isothermal titration calorimetry experiments further revealed that PSHCP also binds single-stranded, double-stranded, and hairpin RNAs. These results provide the first insight into the structure and function of PSHCP, suggesting that PSHCP appears to be an RNA-binding protein that can recognize a broad array of RNA molecules.
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Affiliation(s)
- Katherine M Bauer
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755
| | - Rose Dicovitsky
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755
| | - Maria Pellegrini
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755.,Department of Computer Science, Dartmouth College, Hanover, New Hampshire 03755
| | - Michael J Ragusa
- Department of Biochemistry and Cell Biology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755 .,Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755
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50
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Monk IR, Shaikh N, Begg SL, Gajdiss M, Sharkey LKR, Lee JYH, Pidot SJ, Seemann T, Kuiper M, Winnen B, Hvorup R, Collins BM, Bierbaum G, Udagedara SR, Morey JR, Pulyani N, Howden BP, Maher MJ, McDevitt CA, King GF, Stinear TP. Zinc-binding to the cytoplasmic PAS domain regulates the essential WalK histidine kinase of Staphylococcus aureus. Nat Commun 2019; 10:3067. [PMID: 31296851 PMCID: PMC6624279 DOI: 10.1038/s41467-019-10932-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 06/05/2019] [Indexed: 01/23/2023] Open
Abstract
WalKR (YycFG) is the only essential two-component regulator in the human pathogen Staphylococcus aureus. WalKR regulates peptidoglycan synthesis, but this function alone does not explain its essentiality. Here, to further understand WalKR function, we investigate a suppressor mutant that arose when WalKR activity was impaired; a histidine to tyrosine substitution (H271Y) in the cytoplasmic Per-Arnt-Sim (PASCYT) domain of the histidine kinase WalK. Introducing the WalKH271Y mutation into wild-type S. aureus activates the WalKR regulon. Structural analyses of the WalK PASCYT domain reveal a metal-binding site, in which a zinc ion (Zn2+) is tetrahedrally-coordinated by four amino acids including H271. The WalKH271Y mutation abrogates metal binding, increasing WalK kinase activity and WalR phosphorylation. Thus, Zn2+-binding negatively regulates WalKR. Promoter-reporter experiments using S. aureus confirm Zn2+ sensing by this system. Identification of a metal ligand recognized by the WalKR system broadens our understanding of this critical S. aureus regulon.
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Affiliation(s)
- Ian R Monk
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia.
| | - Nausad Shaikh
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4067, Australia
| | - Stephanie L Begg
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Mike Gajdiss
- University Clinics of Bonn, Institute of Medical Microbiology, Immunology and Parasitology, 53127, Bonn, Germany
| | - Liam K R Sharkey
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Jean Y H Lee
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Sacha J Pidot
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Torsten Seemann
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia.,Melbourne Bioinformatics, University of Melbourne, Melbourne, VIC, 3000, Australia
| | | | | | - Rikki Hvorup
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4067, Australia
| | - Brett M Collins
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4067, Australia
| | - Gabriele Bierbaum
- University Clinics of Bonn, Institute of Medical Microbiology, Immunology and Parasitology, 53127, Bonn, Germany
| | - Saumya R Udagedara
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Jacqueline R Morey
- Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Neha Pulyani
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Megan J Maher
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Christopher A McDevitt
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia.,Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4067, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, 3000, Australia.
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