Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains
| Autor: | Xueqian W. Liu, Delphine Patin, Adam Godzik, Mark W. Knuth, Marc-André Elsliger, Carol L. Farr, Dominique Mengin-Lecreulx, Joanna C Grant, Hsiu-Ju Chiu, Scott A. Lesley, Qingping Xu, Lukasz Jaroszewski, Ian A. Wilson, Ashley M. Deacon |
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| Přispěvatelé: | Stanford Synchrotron Radiation Lightsource (SSRL SLAC), SLAC National Accelerator Laboratory (SLAC), Stanford University-Stanford University, Joint Center for Structural Genomics (JCSG), Stanford University, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, University of California, Genomics Institute of the Novartis Research Foundation, Novartis Research Foundation, Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Center for Research in Biological Systems, University of California [San Diego] (UC San Diego), University of California-University of California, Stanford Synchrotron Radiation Lightsource (SSRL), SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Joint Center for Structural Genomics ( JCSG ), Stanford University [Stanford], Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Sud - Paris 11 ( UP11 ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ), University of California [San Diego] ( UC San Diego ), Bernhardt, Thomas, Pier, Gerald B, Department of Integrative Structural and Computational Biology [Scripps Research Institute], The Scripps Research Institute [La Jolla, San Diego], Sanford Burnham Prebys Medical Discovery Institute, University of California (UC)-University of California (UC) |
| Rok vydání: | 2015 |
| Předmět: |
Models
Molecular Protein Conformation 1.1 Normal biological development and functioning [SDV]Life Sciences [q-bio] DNA Mutational Analysis Lysin Biology Crystallography X-Ray Aminopeptidases Microbiology Amidase Substrate Specificity Cell wall src Homology Domains 03 medical and health sciences chemistry.chemical_compound Bacterial Proteins Underpinning research Models Virology Catalytic Domain Hydrolase Tracheal cytotoxin 2.2 Factors relating to the physical environment Aetiology 030304 developmental biology 0303 health sciences Crystallography [ SDV ] Life Sciences [q-bio] 030306 microbiology Prevention Active site Molecular QR1-502 Biochemistry chemistry biology.protein X-Ray Mutant Proteins Peptidoglycan Peptidoglycan binding Research Article |
| Zdroj: | mBio, vol 6, iss 5 mBio mBio, American Society for Microbiology, 2015, 6 (5), pp.e02327-14. ⟨10.1128/mBio.02327-14⟩ mBio, American Society for Microbiology, 2015, 6 (5), pp.e02327-14. 〈10.1128/mBio.02327-14〉 mBio, Vol 6, Iss 5 (2015) mBio, 2015, 6 (5), pp.e02327-14. ⟨10.1128/mBio.02327-14⟩ |
| ISSN: | 2161-2129 2150-7511 |
| DOI: | 10.1128/mBio.02327-14⟩ |
| Popis: | Bacterial SH3 (SH3b) domains are commonly fused with papain-like Nlp/P60 cell wall hydrolase domains. To understand how the modular architecture of SH3b and NlpC/P60 affects the activity of the catalytic domain, three putative NlpC/P60 cell wall hydrolases were biochemically and structurally characterized. These enzymes all have γ-d-Glu-A2pm (A2pm is diaminopimelic acid) cysteine amidase (or dl-endopeptidase) activities but with different substrate specificities. One enzyme is a cell wall lysin that cleaves peptidoglycan (PG), while the other two are cell wall recycling enzymes that only cleave stem peptides with an N-terminal l-Ala. Their crystal structures revealed a highly conserved structure consisting of two SH3b domains and a C-terminal NlpC/P60 catalytic domain, despite very low sequence identity. Interestingly, loops from the first SH3b domain dock into the ends of the active site groove of the catalytic domain, remodel the substrate binding site, and modulate substrate specificity. Two amino acid differences at the domain interface alter the substrate binding specificity in favor of stem peptides in recycling enzymes, whereas the SH3b domain may extend the peptidoglycan binding surface in the cell wall lysins. Remarkably, the cell wall lysin can be converted into a recycling enzyme with a single mutation. IMPORTANCE Peptidoglycan is a meshlike polymer that envelops the bacterial plasma membrane and bestows structural integrity. Cell wall lysins and recycling enzymes are part of a set of lytic enzymes that target covalent bonds connecting the amino acid and amino sugar building blocks of the PG network. These hydrolases are involved in processes such as cell growth and division, autolysis, invasion, and PG turnover and recycling. To avoid cleavage of unintended substrates, these enzymes have very selective substrate specificities. Our biochemical and structural analysis of three modular NlpC/P60 hydrolases, one lysin, and two recycling enzymes, show that they may have evolved from a common molecular architecture, where the substrate preference is modulated by local changes. These results also suggest that new pathways for recycling PG turnover products, such as tracheal cytotoxin, may have evolved in bacteria in the human gut microbiome that involve NlpC/P60 cell wall hydrolases. |
| Databáze: | OpenAIRE |
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