Computer-based annotation of putative AraC/XylS-family transcription factors of known structure but unknown function

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dc.article.number103132
dc.catalogadoraba
dc.contributor.authorSchüller, Andreas
dc.contributor.authorSlater, A. W.
dc.contributor.authorNorambuena, T.
dc.contributor.authorCifuentes, J. J.
dc.contributor.authorAlmonacid, L. I.
dc.contributor.authorMelo Ledermann, Francisco Javier
dc.date.accessioned2025-02-05T19:46:59Z
dc.date.available2025-02-05T19:46:59Z
dc.date.issued2012
dc.description.abstractCurrently, about 20 crystal structures per day are released and deposited in the Protein Data Bank. A significant fraction of these structures is produced by research groups associated with the structural genomics consortium. The biological function of many of these proteins is generally unknown or not validated by experiment. Therefore, a growing need for functional prediction of protein structures has emerged. Here we present an integrated bioinformatics method that combines sequence-based relationships and three-dimensional (3D) structural similarity of transcriptional regulators with computer prediction of their cognate DNA binding sequences. We applied this method to the AraC/XylS family of transcription factors, which is a large family of transcriptional regulators found in many bacteria controlling the expression of genes involved in diverse biological functions. Three putative new members of this family with known 3D structure but unknown function were identified for which a probable functional classification is provided. Our bioinformatics analyses suggest that they could be involved in plant cell wall degradation (Lin2118 protein from Listeria innocua, PDB code 3oou), symbiotic nitrogen fixation (protein from Chromobacterium violaceum, PDB code 3oio), and either metabolism of plant-derived biomass or nitrogen fixation (protein from Rhodopseudomonas palustris, PDB code 3mn2).
dc.format.extent14 páginas
dc.fuente.origenSIPA
dc.identifier.doi10.1155/2012/103132
dc.identifier.eissn1110-7251
dc.identifier.issn1110-7243
dc.identifier.pubmedid22505803
dc.identifier.pubmedidPMC3312330
dc.identifier.scopusid2-s2.0-84859731351
dc.identifier.urihttps://doi.org/10.1155/2012/103132
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/102160
dc.identifier.wosidWOS:000302648200001
dc.information.autorucFacultad de Ciencias Biológicas; Schüller, Andreas; 0000-0002-4443-4279; 207692
dc.information.autorucFacultad de Ciencias Biológicas; Melo Ledermann, Francisco Javier; 0000-0002-0424-5991; 82342
dc.issue.numeroSpecial Issue: Advanced Computational Methods in Molecular Medicine
dc.language.isoen
dc.nota.accesocontenido completo
dc.pagina.final14
dc.pagina.inicio1
dc.revistaJournal of biomedicine & biotechnology
dc.rightsacceso abierto
dc.rights.licenseAttribution 3.0 Unported
dc.rights.urihttps://creativecommons.org/licenses/by/3.0/
dc.subjectTarget prediction
dc.subjectDrug–target interaction
dc.subjectNetwork-based inference
dc.subjectDrug repositioning
dc.subjectDrug discovery
dc.subject.ddc570
dc.subject.deweyBiologíaes_ES
dc.subject.ods03 Good health and well-being
dc.subject.odspa03 Salud y bienestar
dc.titleComputer-based annotation of putative AraC/XylS-family transcription factors of known structure but unknown function
dc.typeartículo
dc.volumen2012
sipa.codpersvinculados207692
sipa.codpersvinculados82342
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