1
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Amacher JF, Antos JM. Sortases: structure, mechanism, and implications for protein engineering. Trends Biochem Sci 2024:S0968-0004(24)00100-2. [PMID: 38692993 DOI: 10.1016/j.tibs.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/22/2024] [Accepted: 04/15/2024] [Indexed: 05/03/2024]
Abstract
Sortase enzymes are critical cysteine transpeptidases on the surface of bacteria that attach proteins to the cell wall and are involved in the construction of bacterial pili. Due to their ability to recognize specific substrates and covalently ligate a range of reaction partners, sortases are widely used in protein engineering applications via sortase-mediated ligation (SML) strategies. In this review, we discuss recent structural studies elucidating key aspects of sortase specificity and the catalytic mechanism. We also highlight select recent applications of SML, including examples where fundamental studies of sortase structure and function have informed the continued development of these enzymes as tools for protein engineering.
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Affiliation(s)
- Jeanine F Amacher
- Department of Chemistry, Western Washington University, Bellingham, WA 98225, USA.
| | - John M Antos
- Department of Chemistry, Western Washington University, Bellingham, WA 98225, USA.
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2
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Vogel BA, Blount JM, Kodama HM, Goodwin-Rice NJ, Andaluz DJ, Jackson SN, Antos JM, Amacher JF. A unique binding mode of P1' Leu-containing target sequences for Streptococcus pyogenes sortase A results in alternative cleavage. RSC Chem Biol 2024; 5:30-40. [PMID: 38179192 PMCID: PMC10763551 DOI: 10.1039/d3cb00129f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/26/2023] [Indexed: 01/06/2024] Open
Abstract
Sortase enzymes are cysteine transpeptidases that attach environmental sensors, toxins, and other proteins to the cell surface in Gram-positive bacteria. The recognition motif for many sortases is the cell wall sorting signal (CWSS), LPXTG, where X = any amino acid. Recent work from ourselves and others has described recognition of additional amino acids at a number of positions in the CWSS, specifically at the Thr (or P1) and Gly (or P1') positions. In addition, although standard cleavage occurs between these two residues (P1/P1'), we previously observed that the SrtA enzyme from Streptococcus pneumoniae will cleave after the P1' position when its identity is a Leu or Phe. The stereochemical basis of this alternative cleavage is not known, although homologs, e.g., SrtA from Listeria monocytogenes or Staphylococcus aureus do not show alternative cleavage to a significant extent. Here, we use protein biochemistry, structural biology, and computational biochemistry to predict an alternative binding mode that facilitates alternative cleavage. We use Streptococcus pyogenes SrtA (spySrtA) as our model enzyme, first confirming that it shows similar standard/alternative cleavage ratios for LPATL, LPATF, and LPATY sequences. Molecular dynamics simulations suggest that when P1' is Leu, this amino acid binds in the canonical S1 pocket, pushing the P1 Thr towards solvent. The P4 Leu (L̲PATL) binds as it does in standard binding, resulting in a puckered binding conformation. We use P1 Glu-containing peptides to support our hypotheses, and present the complex structure of spySrtA-LPALA to confirm favorable accommodation of Leu in the S1 pocket. Overall, we structurally characterize an alternative binding mode for spySrtA and specific target sequences, expanding the potential protein engineering possibilities in sortase-mediated ligation applications.
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Affiliation(s)
- Brandon A Vogel
- Department of Chemistry, Western Washington University, 516 High St - MS9150 Bellingham WA 98225 USA +1-360-650-2826 +1-360-650-2271 +1-360-650-4397
| | - Jadon M Blount
- Department of Chemistry, Western Washington University, 516 High St - MS9150 Bellingham WA 98225 USA +1-360-650-2826 +1-360-650-2271 +1-360-650-4397
| | - Hanna M Kodama
- Department of Chemistry, Western Washington University, 516 High St - MS9150 Bellingham WA 98225 USA +1-360-650-2826 +1-360-650-2271 +1-360-650-4397
| | - Noah J Goodwin-Rice
- Department of Chemistry, Western Washington University, 516 High St - MS9150 Bellingham WA 98225 USA +1-360-650-2826 +1-360-650-2271 +1-360-650-4397
| | - Devin J Andaluz
- Department of Chemistry, Western Washington University, 516 High St - MS9150 Bellingham WA 98225 USA +1-360-650-2826 +1-360-650-2271 +1-360-650-4397
| | - Sophie N Jackson
- Department of Chemistry, Western Washington University, 516 High St - MS9150 Bellingham WA 98225 USA +1-360-650-2826 +1-360-650-2271 +1-360-650-4397
| | - John M Antos
- Department of Chemistry, Western Washington University, 516 High St - MS9150 Bellingham WA 98225 USA +1-360-650-2826 +1-360-650-2271 +1-360-650-4397
| | - Jeanine F Amacher
- Department of Chemistry, Western Washington University, 516 High St - MS9150 Bellingham WA 98225 USA +1-360-650-2826 +1-360-650-2271 +1-360-650-4397
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3
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Sue CK, Cheung NA, Mahoney BJ, McConnell SA, Scully JM, Fu JY, Chang C, Ton-That H, Loo JA, Clubb RT. The basal and major pilins in the Corynebacterium diphtheriae SpaA pilus adopt similar structures that competitively react with the pilin polymerase. Biopolymers 2024; 115:e23539. [PMID: 37227047 PMCID: PMC11164409 DOI: 10.1002/bip.23539] [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: 01/31/2023] [Revised: 04/12/2023] [Accepted: 04/24/2023] [Indexed: 05/26/2023]
Abstract
Many species of pathogenic gram-positive bacteria display covalently crosslinked protein polymers (called pili or fimbriae) that mediate microbial adhesion to host tissues. These structures are assembled by pilus-specific sortase enzymes that join the pilin components together via lysine-isopeptide bonds. The archetypal SpaA pilus from Corynebacterium diphtheriae is built by the Cd SrtA pilus-specific sortase, which crosslinks lysine residues within the SpaA and SpaB pilins to build the shaft and base of the pilus, respectively. Here, we show that Cd SrtA crosslinks SpaB to SpaA via a K139(SpaB)-T494(SpaA) lysine-isopeptide bond. Despite sharing only limited sequence homology, an NMR structure of SpaB reveals striking similarities with the N-terminal domain of SpaA (N SpaA) that is also crosslinked by Cd SrtA. In particular, both pilins contain similarly positioned reactive lysine residues and adjacent disordered AB loops that are predicted to be involved in the recently proposed "latch" mechanism of isopeptide bond formation. Competition experiments using an inactive SpaB variant and additional NMR studies suggest that SpaB terminates SpaA polymerization by outcompeting N SpaA for access to a shared thioester enzyme-substrate reaction intermediate.
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Affiliation(s)
- Christopher K. Sue
- Department of Chemistry and Biochemistry
- UCLA-DOE Institute for Genomics and Proteomics
| | - Nicole A. Cheung
- UCLA-DOE Institute for Genomics and Proteomics
- Molecular Biology Institute
| | - Brendan J. Mahoney
- Department of Chemistry and Biochemistry
- UCLA-DOE Institute for Genomics and Proteomics
| | - Scott A. McConnell
- Department of Chemistry and Biochemistry
- UCLA-DOE Institute for Genomics and Proteomics
| | - Jack M. Scully
- Department of Chemistry and Biochemistry
- UCLA-DOE Institute for Genomics and Proteomics
| | - Janine Y. Fu
- Department of Chemistry and Biochemistry
- UCLA-DOE Institute for Genomics and Proteomics
| | - Chungyu Chang
- Molecular Biology Institute
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Hung Ton-That
- Molecular Biology Institute
- Division of Oral and Systemic Health Sciences, School of Dentistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry
- UCLA-DOE Institute for Genomics and Proteomics
- Molecular Biology Institute
| | - Robert T. Clubb
- Department of Chemistry and Biochemistry
- UCLA-DOE Institute for Genomics and Proteomics
- Molecular Biology Institute
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4
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Sue CK, Cheung NA, Mahoney BJ, McConnell SA, Scully JM, Fu JY, Chang C, Ton-That H, Loo JA, Clubb RT. The Basal and Major Pilins in the Corynebacterium diphtheriae SpaA Pilus Adopt Similar Structures that Competitively React with the Pilin Polymerase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529612. [PMID: 36865106 PMCID: PMC9980135 DOI: 10.1101/2023.02.23.529612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Many species of pathogenic gram-positive bacteria display covalently crosslinked protein polymers (called pili or fimbriae) that mediate microbial adhesion to host tissues. These structures are assembled by pilus-specific sortase enzymes that join the pilin components together via lysine-isopeptide bonds. The archetypal SpaA pilus from Corynebacterium diphtheriae is built by the Cd SrtA pilus-specific sortase, which crosslinks lysine residues within the SpaA and SpaB pilins to build the shaft and base of the pilus, respectively. Here, we show that Cd SrtA crosslinks SpaB to SpaA via a K139(SpaB)-T494(SpaA) lysine-isopeptide bond. Despite sharing only limited sequence homology, an NMR structure of SpaB reveals striking similarities with the N-terminal domain of SpaA ( N SpaA) that is also crosslinked by Cd SrtA. In particular, both pilins contain similarly positioned reactive lysine residues and adjacent disordered AB loops that are predicted to be involved in the recently proposed "latch" mechanism of isopeptide bond formation. Competition experiments using an inactive SpaB variant and additional NMR studies suggest that SpaB terminates SpaA polymerization by outcompeting N SpaA for access to a shared thioester enzyme-substrate reaction intermediate.
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5
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Structures of Streptococcus pyogenes Class A sortase in complex with substrate and product mimics provide key details of target recognition. J Biol Chem 2022; 298:102446. [PMID: 36055407 PMCID: PMC9520033 DOI: 10.1016/j.jbc.2022.102446] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 12/02/2022] Open
Abstract
The cell wall is a critical extracellular barrier for bacteria and many other organisms. In bacteria, this structural layer consists of peptidoglycan, which maintains cell shape and structural integrity and provides a scaffold for displaying various protein factors. To attach proteins to the cell wall, Gram-positive bacteria utilize sortase enzymes, which are cysteine transpeptidases that recognize and cleave a specific sorting signal, followed by ligation of the sorting signal–containing protein to the peptidoglycan precursor lipid II (LII). This mechanism is the subject of considerable interest as a target for therapeutic intervention and as a tool for protein engineering, where sortases have enabled sortase-mediated ligation or sortagging strategies. Despite these uses, there remains an incomplete understanding of the stereochemistry of substrate recognition and ligation product formation. Here, we solved the first structures of sortase A from Streptococcus pyogenes bound to two substrate sequences, LPATA and LPATS. In addition, we synthesized a mimetic of the product of sortase-mediated ligation involving LII (LPAT-LII) and solved the complex structure in two ligand conformations. These structures were further used as the basis for molecular dynamics simulations to probe sortase A-ligand dynamics and to construct a model of the acyl–enzyme intermediate, thus providing a structural view of multiple key states in the catalytic mechanism. Overall, this structural information provides new insights into the recognition of the sortase substrate motif and LII ligation partner and will support the continued development of sortases for protein engineering applications.
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Kumar V, Murmu S, Krishnan V. Deciphering the substrate specificity of housekeeping sortase A and pilus-specific sortase C of probiotic bacterium Lactococcus lactis. Biochimie 2022; 200:140-152. [PMID: 35654243 DOI: 10.1016/j.biochi.2022.05.017] [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: 01/28/2022] [Revised: 04/25/2022] [Accepted: 05/26/2022] [Indexed: 11/02/2022]
Abstract
Several strains and species of lactic acid bacteria (LAB) are widely used in fermented foods, including dairy products and also as probiotics, because of their contribution to various health benefits in humans. Sortase enzymes decorate the bacterial cell wall with different surface proteins and pili for facilitating the interactions with host and environment for the colonization and beneficial effects. While the sortases and sortase anchored proteins from pathogens have been the prime focus of the research in the past, sortases from many non-pathogenic bacteria, including LAB strains, have attracted attention for their potential applications in vaccine delivery and other clinical interventions. Here, we report the purification and functional characterization of two sortases (housekeeping SrtA and pilus-specific SrtC) from a probiotic Lactococcus lactis. The purified sortases were found to be active against the putative LPXTG motif-based peptide substrates, albeit with differences. The in-silico analysis provides insights into the residues involved in substrate binding and specificity. Overall, this study sheds new light on the aspects of structure, substrate specificity, and function of sortases from non-pathogenic bacteria, which may have physiological ramifications as well as their applications in sortase-mediated protein bioconjugation.
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Affiliation(s)
- Vijay Kumar
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, Haryana (NCR Delhi), India
| | - Sumit Murmu
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, Haryana (NCR Delhi), India
| | - Vengadesan Krishnan
- Laboratory of Structural Microbiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, Haryana (NCR Delhi), India.
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Gao M, Johnson DA, Piper IM, Kodama HM, Svendsen JE, Tahti E, Longshore‐Neate F, Vogel B, Antos JM, Amacher JF. Structural and biochemical analyses of selectivity determinants in chimeric Streptococcus Class A sortase enzymes. Protein Sci 2022; 31:701-715. [PMID: 34939250 PMCID: PMC8862441 DOI: 10.1002/pro.4266] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 01/22/2023]
Abstract
Sequence variation in related proteins is an important characteristic that modulates activity and selectivity. An example of a protein family with a large degree of sequence variation is that of bacterial sortases, which are cysteine transpeptidases on the surface of gram-positive bacteria. Class A sortases are responsible for attachment of diverse proteins to the cell wall to facilitate environmental adaption and interaction. These enzymes are also used in protein engineering applications for sortase-mediated ligations (SML) or sortagging of protein targets. We previously investigated SrtA from Streptococcus pneumoniae, identifying a number of putative β7-β8 loop-mediated interactions that affected in vitro enzyme function. We identified residues that contributed to the ability of S. pneumoniae SrtA to recognize several amino acids at the P1' position of the substrate motif, underlined in LPXTG, in contrast to the strict P1' Gly recognition of SrtA from Staphylococcus aureus. However, motivated by the lack of a structural model for the active, monomeric form of S. pneumoniae SrtA, here, we expanded our studies to other Streptococcus SrtA proteins. We solved the first monomeric structure of S. agalactiae SrtA which includes the C-terminus, and three others of β7-β8 loop chimeras from S. pyogenes and S. agalactiae SrtA. These structures and accompanying biochemical data support our previously identified β7-β8 loop-mediated interactions and provide additional insight into their role in Class A sortase substrate selectivity. A greater understanding of individual SrtA sequence and structural determinants of target selectivity may also facilitate the design or discovery of improved sortagging tools.
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Affiliation(s)
- Melody Gao
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - D. Alex Johnson
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Isabel M. Piper
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Hanna M. Kodama
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Justin E. Svendsen
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Elise Tahti
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | | | - Brandon Vogel
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - John M. Antos
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
| | - Jeanine F. Amacher
- Department of ChemistryWestern Washington UniversityBellinghamWashingtonUSA
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8
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Kumari P, Bowmik S, Paul SK, Biswas B, Banerjee SK, Murty US, Ravichandiran V, Mohan U. Sortase A: A chemoenzymatic approach for the labeling of cell surfaces. Biotechnol Bioeng 2021; 118:4577-4589. [PMID: 34491580 DOI: 10.1002/bit.27935] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/20/2021] [Accepted: 08/27/2021] [Indexed: 01/31/2023]
Abstract
Sortase A, a transpeptidase enzyme is present in many Gram-positive bacteria and helps in the recruitment of the cell surface proteins. Over the last two decades, Sortase A has become an attractive tool for performing in vivo and in vitro ligations. Sortase A-mediated ligation has continuously been used for its specificity, robustness, and highly efficient nature. These properties make it a popular choice among protein engineers as well as researchers from different fields. In this review, we give an overview of Sortase A-mediated ligation of various molecules on the cell surfaces, which can have diverse applications in interdisciplinary fields.
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Affiliation(s)
- Poonam Kumari
- Department of Biotechnology, National Institute of Pharmaceutical Education & Research (NIPER), Guwahati, Assam, India
| | - Sujoy Bowmik
- Department of Biotechnology, National Institute of Pharmaceutical Education & Research (NIPER), Guwahati, Assam, India
| | - Sudipto Kumar Paul
- Department of Biotechnology, National Institute of Pharmaceutical Education & Research (NIPER), Guwahati, Assam, India
| | - Bidisha Biswas
- Department of Biotechnology, National Institute of Pharmaceutical Education & Research (NIPER), Guwahati, Assam, India
| | - Sanjay K Banerjee
- Department of Biotechnology, National Institute of Pharmaceutical Education & Research (NIPER), Guwahati, Assam, India
| | | | - Velayutham Ravichandiran
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education & Research (NIPER), Kolkata, West Bengal, India
| | - Utpal Mohan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education & Research (NIPER), Kolkata, West Bengal, India
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9
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Sequence variation in the β7-β8 loop of bacterial class A sortase enzymes alters substrate selectivity. J Biol Chem 2021; 297:100981. [PMID: 34302812 PMCID: PMC8361268 DOI: 10.1016/j.jbc.2021.100981] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/09/2021] [Accepted: 07/16/2021] [Indexed: 01/03/2023] Open
Abstract
Gram-positive bacteria contain sortase enzymes on their cell surfaces that catalyze transpeptidation reactions critical for proper cellular function. In vitro, sortases are used in sortase-mediated ligation (SML) reactions for a variety of protein engineering applications. Historically, sortase A from Staphylococcus aureus (saSrtA) has been the enzyme of choice to catalyze SML reactions. However, the stringent specificity of saSrtA for the LPXTG sequence motif limits its uses. Here, we describe the impact on substrate selectivity of a structurally conserved loop with a high degree of sequence variability in all classes of sortases. We investigate the contribution of this β7–β8 loop by designing and testing chimeric sortase enzymes. Our chimeras utilize natural sequence variation of class A sortases from eight species engineered into the SrtA sequence from Streptococcus pneumoniae. While some of these chimeric enzymes mimic the activity and selectivity of the WT protein from which the loop sequence was derived (e.g., that of saSrtA), others results in chimeric Streptococcus pneumoniae SrtA enzymes that are able to accommodate a range of residues in the final position of the substrate motif (LPXTX). Using mutagenesis, structural comparisons, and sequence analyses, we identify three interactions facilitated by β7–β8 loop residues that appear to be broadly conserved or converged upon in class A sortase enzymes. These studies provide the foundation for a deeper understanding of sortase target selectivity and can expand the sortase toolbox for future SML applications.
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10
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Selvaraj C, Selvaraj G, Mohamed Ismail R, Vijayakumar R, Baazeem A, Wei DQ, Singh SK. Interrogation of Bacillus anthracis SrtA active site loop forming open/close lid conformations through extensive MD simulations for understanding binding selectivity of SrtA inhibitors. Saudi J Biol Sci 2021; 28:3650-3659. [PMID: 34220215 PMCID: PMC8241892 DOI: 10.1016/j.sjbs.2021.05.009] [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] [Received: 04/15/2021] [Revised: 04/25/2021] [Accepted: 05/02/2021] [Indexed: 02/07/2023] Open
Abstract
Bacillus anthracis is a gram positive, deadly spore forming bacteria causing anthrax and these bacteria having the complex mechanism in the cell wall envelope, which can adopt the changes in environmental conditions. In this, the membrane bound cell wall proteins are said to progressive drug target for the inhibition of Bacillus anthracis. Among the cell wall proteins, the SrtA is one of the important mechanistic protein, which mediate the ligation with LPXTG motif by forming the amide bonds. The SrtA plays the vital role in cell signalling, cell wall formation, and biofilm formations. Inhibition of SrtA leads to rupture of the cell wall and biofilm formation, and that leads to inhibition of Bacillus anthracis and thus, SrtA is core important enzyme to study the inhibition mechanism. In this study, we have examined 28 compounds, which have the inhibitory activity against the Bacillus anthracis SrtA for developing the 3D-QSAR and also, compounds binding selectivity with both open and closed SrtA conformations, obtained from 100 ns of MD simulations. The binding site loop deviate in forming the open and closed gate mechanism is investigated to understand the inhibitory profile of reported compounds, and results show the closed state active site conformations are required for ligand binding specificity. Overall, the present study may offer an opportunity for better understanding of the mechanism of action and can be aided to further designing of a novel and highly potent SrtA inhibitors.
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Affiliation(s)
- Chandrabose Selvaraj
- Department of Bioinformatics, Computer Aided Drug Design and Molecular Modelling Lab, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
- Corresponding authors.
| | - Gurudeeban Selvaraj
- Centre for Research in Molecular Modelling, Concordia University, 5618 Montreal, Quebec, Canada
| | - Randa Mohamed Ismail
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah 11952, Saudi Arabia
- Department of Microbiology and Immunology, Veterinary Research Division, National Research Center (NRC), Giza, Egypt
| | - Rajendran Vijayakumar
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah 11952, Saudi Arabia
| | - Alaa Baazeem
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sanjeev Kumar Singh
- Department of Bioinformatics, Computer Aided Drug Design and Molecular Modelling Lab, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
- Corresponding authors.
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11
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Sortase-assembled pili in Corynebacterium diphtheriae are built using a latch mechanism. Proc Natl Acad Sci U S A 2021; 118:2019649118. [PMID: 33723052 DOI: 10.1073/pnas.2019649118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Gram-positive bacteria assemble pili (fimbriae) on their surfaces to adhere to host tissues and to promote polymicrobial interactions. These hair-like structures, although very thin (1 to 5 nm), exhibit impressive tensile strengths because their protein components (pilins) are covalently crosslinked together via lysine-isopeptide bonds by pilus-specific sortase enzymes. While atomic structures of isolated pilins have been determined, how they are joined together by sortases and how these interpilin crosslinks stabilize pilus structure are poorly understood. Using a reconstituted pilus assembly system and hybrid structural biology methods, we elucidated the solution structure and dynamics of the crosslinked interface that is repeated to build the prototypical SpaA pilus from Corynebacterium diphtheriae We show that sortase-catalyzed introduction of a K190-T494 isopeptide bond between adjacent SpaA pilins causes them to form a rigid interface in which the LPLTG sorting signal is inserted into a large binding groove. Cellular and quantitative kinetic measurements of the crosslinking reaction shed light onto the mechanism of pilus biogenesis. We propose that the pilus-specific sortase in C. diphtheriae uses a latch mechanism to select K190 on SpaA for crosslinking in which the sorting signal is partially transferred from the enzyme to a binding groove in SpaA in order to facilitate catalysis. This process is facilitated by a conserved loop in SpaA, which after crosslinking forms a stabilizing latch that covers the K190-T494 isopeptide bond. General features of the structure and sortase-catalyzed assembly mechanism of the SpaA pilus are likely conserved in Gram-positive bacteria.
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12
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Chateau A, Van der Verren SE, Remaut H, Fioravanti A. The Bacillus anthracis Cell Envelope: Composition, Physiological Role, and Clinical Relevance. Microorganisms 2020; 8:E1864. [PMID: 33255913 PMCID: PMC7759979 DOI: 10.3390/microorganisms8121864] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/23/2020] [Accepted: 11/24/2020] [Indexed: 12/31/2022] Open
Abstract
Anthrax is a highly resilient and deadly disease caused by the spore-forming bacterial pathogen Bacillus anthracis. The bacterium presents a complex and dynamic composition of its cell envelope, which changes in response to developmental and environmental conditions and host-dependent signals. Because of their easy to access extracellular locations, B. anthracis cell envelope components represent interesting targets for the identification and development of novel therapeutic and vaccine strategies. This review will focus on the novel insights regarding the composition, physiological role, and clinical relevance of B. anthracis cell envelope components.
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Affiliation(s)
- Alice Chateau
- Avignon Université, INRAE, UMR SQPOV, F-84914 Avignon, France;
| | - Sander E. Van der Verren
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium; (S.E.V.d.V.); (H.R.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Han Remaut
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium; (S.E.V.d.V.); (H.R.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Antonella Fioravanti
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, 1050 Brussels, Belgium; (S.E.V.d.V.); (H.R.)
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
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13
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Wójcik M, Szala K, van Merkerk R, Quax WJ, Boersma YL. Engineering the specificity of Streptococcus pyogenes sortase A by loop grafting. Proteins 2020; 88:1394-1400. [PMID: 32501594 PMCID: PMC7586933 DOI: 10.1002/prot.25958] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/30/2020] [Accepted: 05/27/2020] [Indexed: 11/24/2022]
Abstract
Sortases are a group of enzymes displayed on the cell‐wall of Gram‐positive bacteria. They are responsible for the attachment of virulence factors onto the peptidoglycan in a transpeptidation reaction through recognition of a pentapeptide substrate. Most housekeeping sortases recognize one specific pentapeptide motif; however, Streptococcus pyogenes sortase A (SpSrtA WT) recognizes LPETG, LPETA and LPKLG motifs. Here, we examined SpSrtA's flexible substrate specificity by investigating the role of the β7/β8 loop in determining substrate specificity. We exchanged the β7/β8 loop in SpSrtA with corresponding β7/β8 loops from Staphylococcus aureus (SaSrtA WT) and Bacillus anthracis (BaSrtA WT). While the BaSrtA‐derived variant showed no enzymatic activity toward either LPETG or LPETA substrates, the activity of the SaSrtA‐derived mutant toward the LPETA substrate was completely abolished. Instead, the mutant had an improved activity toward LPETG, the preferred substrate of SaSrtA WT.
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Affiliation(s)
- Magdalena Wójcik
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Kamil Szala
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Ronald van Merkerk
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Wim J Quax
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Ykelien L Boersma
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
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14
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Sue CK, McConnell SA, Ellis-Guardiola K, Muroski J, McAllister RA, Yu J, Alvarez AI, Chang C, Ogorzalek Loo RR, Loo JA, Ton-That H, Clubb RT. Kinetics and Optimization of the Lysine-Isopeptide Bond Forming Sortase Enzyme from Corynebacterium diphtheriae. Bioconjug Chem 2020; 31:1624-1634. [PMID: 32396336 PMCID: PMC8153732 DOI: 10.1021/acs.bioconjchem.0c00163] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Site-specifically modified protein bioconjugates have important applications in biology, chemistry, and medicine. Functionalizing specific protein side chains with enzymes using mild reaction conditions is of significant interest, but remains challenging. Recently, the lysine-isopeptide bond forming activity of the sortase enzyme that builds surface pili in Corynebacterium diphtheriae (CdSrtA) has been reconstituted in vitro. A mutationally activated form of CdSrtA was shown to be a promising bioconjugating enzyme that can attach Leu-Pro-Leu-Thr-Gly peptide fluorophores to a specific lysine residue within the N-terminal domain of the SpaA protein (NSpaA), enabling the labeling of target proteins that are fused to NSpaA. Here we present a detailed analysis of the CdSrtA catalyzed protein labeling reaction. We show that the first step in catalysis is rate limiting, which is the formation of the CdSrtA-peptide thioacyl intermediate that subsequently reacts with a lysine ε-amine in NSpaA. This intermediate is surprisingly stable, limiting spurious proteolysis of the peptide substrate. We report the discovery of a new enzyme variant (CdSrtAΔ) that has significantly improved transpeptidation activity, because it completely lacks an inhibitory polypeptide appendage ("lid") that normally masks the active site. We show that the presence of the lid primarily impairs formation of the thioacyl intermediate and not the recognition of the NSpaA substrate. Quantitative measurements reveal that CdSrtAΔ generates its cross-linked product with a catalytic turnover number of 1.4 ± 0.004 h-1 and that it has apparent KM values of 0.16 ± 0.04 and 1.6 ± 0.3 mM for its NSpaA and peptide substrates, respectively. CdSrtAΔ is 7-fold more active than previously studied variants, labeling >90% of NSpaA with peptide within 6 h. The results of this study further improve the utility of CdSrtA as a protein labeling tool and provide insight into the enzyme catalyzed reaction that underpins protein labeling and pilus biogenesis.
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Affiliation(s)
- Christopher K. Sue
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Scott A. McConnell
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Ken Ellis-Guardiola
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - John Muroski
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Rachel A. McAllister
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Justin Yu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Ana I. Alvarez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Chungyu Chang
- Molecular Biology Institute and the University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Rachel R. Ogorzalek Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- Molecular Biology Institute and the University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Hung Ton-That
- Molecular Biology Institute and the University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
| | - Robert T. Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
- Molecular Biology Institute and the University of California, Los Angeles, 611 Charles Young Drive East, Los Angeles, CA 90095
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15
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Kang CY, Huang IH, Chou CC, Wu TY, Chang JC, Hsiao YY, Cheng CH, Tsai WJ, Hsu KC, Wang S. Functional analysis of Clostridium difficile sortase B reveals key residues for catalytic activity and substrate specificity. J Biol Chem 2020; 295:3734-3745. [PMID: 32005667 PMCID: PMC7076211 DOI: 10.1074/jbc.ra119.011322] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 01/31/2020] [Indexed: 01/07/2023] Open
Abstract
Most of Gram-positive bacteria anchor surface proteins to the peptidoglycan cell wall by sortase, a cysteine transpeptidase that targets proteins displaying a cell wall sorting signal. Unlike other bacteria, Clostridium difficile, the major human pathogen responsible for antibiotic-associated diarrhea, has only a single functional sortase (SrtB). Sortase's vital importance in bacterial virulence has been long recognized, and C. difficile sortase B (Cd-SrtB) has become an attractive therapeutic target for managing C. difficile infection. A better understanding of the molecular activity of Cd-SrtB may help spur the development of effective agents against C. difficile infection. In this study, using site-directed mutagenesis, biochemical and biophysical tools, LC-MS/MS, and crystallographic analyses, we identified key residues essential for Cd-SrtB catalysis and substrate recognition. To the best of our knowledge, we report the first evidence that a conserved serine residue near the active site participates in the catalytic activity of Cd-SrtB and also SrtB from Staphylococcus aureus The serine residue indispensable for SrtB activity may be involved in stabilizing a thioacyl-enzyme intermediate because it is neither a nucleophilic residue nor a substrate-interacting residue, based on the LC-MS/MS data and available structural models of SrtB-substrate complexes. Furthermore, we also demonstrated that residues 163-168 located on the β6/β7 loop of Cd-SrtB dominate specific recognition of the peptide substrate PPKTG. The results of this work reveal key residues with roles in catalysis and substrate specificity of Cd-SrtB.
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Affiliation(s)
- Chia-Yu Kang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan
| | - I-Hsiu Huang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan
| | - Chi-Chi Chou
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Tsai-Yu Wu
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan
| | - Jyun-Cyuan Chang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan
| | - Yu-Yuan Hsiao
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan,Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu 300, Taiwan
| | - Cheng-Hsuan Cheng
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan,Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Wei-Jiun Tsai
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan,Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
| | - Kai-Cheng Hsu
- Graduate Institute of Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Shuying Wang
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan,Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan,Institute of Basic Medical Science, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, To whom correspondence should be addressed:
Dept. of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan. Tel.:
886-6-2353535, Ext. 5634; Fax:
886-6-2082705; E-mail:
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16
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A comprehensive in silico analysis of sortase superfamily. J Microbiol 2019; 57:431-443. [DOI: 10.1007/s12275-019-8545-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/02/2019] [Accepted: 01/10/2019] [Indexed: 12/22/2022]
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17
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Jacobitz AW, Kattke MD, Wereszczynski J, Clubb RT. Sortase Transpeptidases: Structural Biology and Catalytic Mechanism. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 109:223-264. [PMID: 28683919 DOI: 10.1016/bs.apcsb.2017.04.008] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Gram-positive bacteria use sortase cysteine transpeptidase enzymes to covalently attach proteins to their cell wall and to assemble pili. In pathogenic bacteria sortases are potential drug targets, as many of the proteins that they display on the microbial surface play key roles in the infection process. Moreover, the Staphylococcus aureus Sortase A (SaSrtA) enzyme has been developed into a valuable biochemical reagent because of its ability to ligate biomolecules together in vitro via a covalent peptide bond. Here we review what is known about the structures and catalytic mechanism of sortase enzymes. Based on their primary sequences, most sortase homologs can be classified into six distinct subfamilies, called class A-F enzymes. Atomic structures reveal unique, class-specific variations that support alternate substrate specificities, while structures of sortase enzymes bound to sorting signal mimics shed light onto the molecular basis of substrate recognition. The results of computational studies are reviewed that provide insight into how key reaction intermediates are stabilized during catalysis, as well as the mechanism and dynamics of substrate recognition. Lastly, the reported in vitro activities of sortases are compared, revealing that the transpeptidation activity of SaSrtA is at least 20-fold faster than other sortases that have thus far been characterized. Together, the results of the structural, computational, and biochemical studies discussed in this review begin to reveal how sortases decorate the microbial surface with proteins and pili, and may facilitate ongoing efforts to discover therapeutically useful small molecule inhibitors.
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Affiliation(s)
- Alex W Jacobitz
- The Molecular Biology Institute and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, United States
| | - Michele D Kattke
- The Molecular Biology Institute and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, United States
| | - Jeff Wereszczynski
- Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, IL, United States
| | - Robert T Clubb
- The Molecular Biology Institute and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, CA, United States.
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18
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Kattke MD, Chan AH, Duong A, Sexton DL, Sawaya MR, Cascio D, Elliot MA, Clubb RT. Crystal Structure of the Streptomyces coelicolor Sortase E1 Transpeptidase Provides Insight into the Binding Mode of the Novel Class E Sorting Signal. PLoS One 2016; 11:e0167763. [PMID: 27936128 PMCID: PMC5148588 DOI: 10.1371/journal.pone.0167763] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/18/2016] [Indexed: 01/17/2023] Open
Abstract
Many species of Gram-positive bacteria use sortase transpeptidases to covalently affix proteins to their cell wall or to assemble pili. Sortase-displayed proteins perform critical and diverse functions for cell survival, including cell adhesion, nutrient acquisition, and morphological development, among others. Based on their amino acid sequences, there are at least six types of sortases (class A to F enzymes); however, class E enzymes have not been extensively studied. Class E sortases are used by soil and freshwater-dwelling Actinobacteria to display proteins that contain a non-canonical LAXTG sorting signal, which differs from 90% of known sorting signals by substitution of alanine for proline. Here we report the first crystal structure of a class E sortase, the 1.93 Å resolution structure of the SrtE1 enzyme from Streptomyces coelicolor. The active site is bound to a tripeptide, providing insight into the mechanism of substrate binding. SrtE1 possesses β3/β4 and β6/β7 active site loops that contact the LAXTG substrate and are structurally distinct from other classes. We propose that SrtE1 and other class E sortases employ a conserved tyrosine residue within their β3/β4 loop to recognize the amide nitrogen of alanine at position P3 of the sorting signal through a hydrogen bond, as seen here. Incapability of hydrogen-bonding with canonical proline-containing sorting signals likely contributes to class E substrate specificity. Furthermore, we demonstrate that surface anchoring of proteins involved in aerial hyphae formation requires an N-terminal segment in SrtE1 that is presumably positioned within the cytoplasm. Combined, our results reveal unique features within class E enzymes that enable them to recognize distinct sorting signals, and could facilitate the development of substrate-based inhibitors of this important enzyme family.
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Affiliation(s)
- Michele D. Kattke
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Albert H. Chan
- Department of Pharmacology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Andrew Duong
- Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Danielle L. Sexton
- Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Michael R. Sawaya
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Duilio Cascio
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Marie A. Elliot
- Department of Biology and Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Robert T. Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, United States of America
- UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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19
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Jacobitz AW, Naziga EB, Yi SW, McConnell SA, Peterson R, Jung ME, Clubb RT, Wereszczynski J. The "Lid" in the Streptococcus pneumoniae SrtC1 Sortase Adopts a Rigid Structure that Regulates Substrate Access to the Active Site. J Phys Chem B 2016; 120:8302-12. [PMID: 27109553 DOI: 10.1021/acs.jpcb.6b01930] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Many species of Gram-positive bacteria use sortase enzymes to assemble long, proteinaceous pili structures that project from the cell surface to mediate microbial adhesion. Sortases construct highly stable structures by catalyzing a transpeptidation reaction that covalently links pilin subunits together via isopeptide bonds. Most Gram-positive pili are assembled by class C sortases that contain a "lid", a structurally unique N-terminal extension that occludes the active site. It has been hypothesized that the "lid" in many sortases is mobile and thus capable of readily being displaced from the enzyme to facilitate substrate binding. Here, we show using NMR dynamics measurements, in vitro assays, and molecular dynamics simulations that the lid in the class C sortase from Streptococcus pneumoniae (SrtC1) adopts a rigid conformation in solution that is devoid of large magnitude conformational excursions that occur on mechanistically relevant time scales. Additionally, we show that point mutations in the lid induce dynamic behavior that correlates with increased hydrolytic activity and sorting signal substrate access to the active site cysteine residue. These results suggest that the lid of the S. pneumoniae SrtC1 enzyme has a negative regulatory function and imply that a significant energetic barrier must be surmounted by currently unidentified factors to dislodge it from the active site to initiate pilus biogenesis.
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Affiliation(s)
- Alex W Jacobitz
- Department of Chemistry and Biochemistry and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles , 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Emmanuel B Naziga
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , 3440 South Dearborn Street, Chicago, Illinois 60616, United States
| | - Sung Wook Yi
- Department of Chemistry and Biochemistry and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles , 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Scott A McConnell
- Department of Chemistry and Biochemistry and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles , 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Robert Peterson
- Department of Chemistry and Biochemistry and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles , 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Michael E Jung
- Department of Chemistry and Biochemistry and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles , 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Robert T Clubb
- Department of Chemistry and Biochemistry and the UCLA-DOE Institute of Genomics and Proteomics, University of California, Los Angeles , 611 Charles E. Young Drive East, Los Angeles, California 90095-1570, United States
| | - Jeff Wereszczynski
- Department of Physics and Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology , 3440 South Dearborn Street, Chicago, Illinois 60616, United States
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