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dc.contributor.authorRendón Ramírez, Adela
dc.contributor.authorShukla, Manish
dc.contributor.authorOda, Masataka
dc.contributor.authorChakraborty, Sandeep
dc.contributor.authorMinda, Renu
dc.contributor.authorDandekar, Abhaya M.
dc.contributor.authorAsgeirsson, Bjarni
dc.contributor.authorGoñi Urcelay, Félix María
dc.contributor.authorRao, Basuthkar J.
dc.date.accessioned2014-02-05T17:50:43Z
dc.date.available2014-02-05T17:50:43Z
dc.date.issued2013-08
dc.identifier.citationPLoS ONE 8(8) : (2013) // e70923es
dc.identifier.issn1932-6203
dc.identifier.urihttp://hdl.handle.net/10810/11361
dc.description.abstractProteolytic enzymes have evolved several mechanisms to cleave peptide bonds. These distinct types have been systematically categorized in the MEROPS database. While a BLAST search on these proteases identifies homologous proteins, sequence alignment methods often fail to identify relationships arising from convergent evolution, exon shuffling, and modular reuse of catalytic units. We have previously established a computational method to detect functions in proteins based on the spatial and electrostatic properties of the catalytic residues (CLASP). CLASP identified a promiscuous serine protease scaffold in alkaline phosphatases (AP) and a scaffold recognizing a beta-lactam (imipenem) in a cold-active Vibrio AP. Subsequently, we defined a methodology to quantify promiscuous activities in a wide range of proteins. Here, we assemble a module which encapsulates the multifarious motifs used by protease families listed in the MEROPS database. Since APs and proteases are an integral component of outer membrane vesicles (OMV), we sought to query other OMV proteins, like phospholipase C (PLC), using this search module. Our analysis indicated that phosphoinositide-specific PLC from Bacillus cereus is a serine protease. This was validated by protease assays, mass spectrometry and by inhibition of the native phospholipase activity of PI-PLC by the well-known serine protease inhibitor AEBSF (IC50 = 0.018 mM). Edman degradation analysis linked the specificity of the protease activity to a proline in the amino terminal, suggesting that the PI-PLC is a prolyl peptidase. Thus, we propose a computational method of extending protein families based on the spatial and electrostatic congruence of active site residues.es
dc.description.sponsorshipBJR would like to thank the Tata Institute of Fundamental Research (Department of Atomic Energy) for financial support. MO was supported in part by a Grant-in-aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan; (grant No. 21790431). FMG thanks the Spanish Ministerio de Ciencia e Innovacion for grant No. BFU 2007/62062, and the University of the Basque Country for grant No. IT 461-07. BA extends gratitude to the Icelandic National Research Council and the University of Iceland Research Found for supporting the project financially. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.es
dc.language.isoenges
dc.publisherPublic Library Sciencees
dc.relationinfo:eu-repo/grantAgreement/MICINN/BFU2007-62062
dc.relationinfo:eu-repo/grantAgreement/MICINN/BFU2007-62062
dc.rightsinfo:eu-repo/semantics/openAccesses
dc.subjectperfringens alpha toxines
dc.subjectouter membrane vesicleses
dc.subjectphospholipase-Ces
dc.subjectalkaline phosphatasees
dc.subjectconvergent evolutiones
dc.subjectsphingomyelinase activitieses
dc.subjectbacterial phospholipaseses
dc.subjectpseudomonas aeruginosaes
dc.subjectcysteine proteaseses
dc.subjectcrystal structurees
dc.titleA Computational Module Assembled from Different Protease Family Motifs Identifies PI PLC from Bacillus cereus as a Putative Prolyl Peptidase with a Serine Protease Scaffoldes
dc.typeinfo:eu-repo/semantics/articlees
dc.rights.holder© 2013 Rendón-Ramirez et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.es
dc.relation.publisherversionhttp://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0070923es
dc.identifier.doi10.1371/journal.pone.0070923
dc.departamentoesBioquímica y biología moleculares_ES
dc.departamentoeuBiokimika eta biologia molekularraes_ES
dc.subject.categoriaAGRICULTURAL AND BIOLOGICAL SCIENCES
dc.subject.categoriaMEDICINE
dc.subject.categoriaBIOCHEMISTRY AND MOLECULAR BIOLOGY


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