Computer-Based Annotation of Putative AraC/XylS-Family Transcription Factors of Known Structure but Unknown Function

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dc.contributor.authorSchueller, Andreas
dc.contributor.authorSlater, Alex W.
dc.contributor.authorNorambuena, Tomas
dc.contributor.authorCifuentes, Juan J.
dc.contributor.authorAlmonacid, Leonardo I.
dc.contributor.authorMelo, Francisco
dc.date.accessioned2024-01-10T13:47:04Z
dc.date.available2024-01-10T13:47:04Z
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.description.funderFONDECYT (Fondo Nacional de Desarrollo Cientifico y Tecnologico, Chile)
dc.description.funderCONICYT (Comision Nacional de Investigacion Cientifica y Tecnologica, Chile)
dc.description.funderICM (Iniciativa Cientifica Milenio, Chile)
dc.fechaingreso.objetodigital2024-05-10
dc.format.extent14 páginas
dc.fuente.origenWOS
dc.identifier.doi10.1155/2012/103132
dc.identifier.eissn1110-7251
dc.identifier.issn1110-7243
dc.identifier.pubmedidMEDLINE:22505803
dc.identifier.urihttps://doi.org/10.1155/2012/103132
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/79231
dc.identifier.wosidWOS:000302648200001
dc.information.autorucCiencias Biológicas;Cifuentes J;S/I;218002
dc.information.autorucCiencias Biológicas;Melo F;S/I;82342
dc.information.autorucCiencias Biológicas;Norambuena T;S/I;121728
dc.information.autorucCiencias Biológicas;Schuller A;S/I;207692
dc.information.autorucCiencias Biológicas;Slater A;S/I;132730
dc.language.isoen
dc.nota.accesocontenido completo
dc.publisherHINDAWI LTD
dc.revistaJOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY
dc.rightsacceso abierto
dc.subjectDNA-BINDING DOMAIN
dc.subjectESCHERICHIA-COLI
dc.subjectRHODOBACTER-CAPSULATUS
dc.subjectALIGNMENT
dc.subjectSEQUENCE
dc.subjectACTIVATION
dc.subjectSYSTEM
dc.subjectFOLD
dc.subjectDEGRADATION
dc.subjectVERSATILE
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
sipa.codpersvinculados218002
sipa.codpersvinculados82342
sipa.codpersvinculados121728
sipa.codpersvinculados207692
sipa.codpersvinculados132730
sipa.indexWOS
sipa.indexScopus
sipa.trazabilidadCarga SIPA;09-01-2024
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