title: Computer-based annotation of putative AraC/XylS-family transcription factors of known structure but unknown function.
abstract: Currently, 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).
authors.affiliation: Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, 8331150 Santiago, Chile.
authors.forename: Andreas
authors.initials: A
authors.lastname: Schüller
authors.forename: Alex W
authors.initials: AW
authors.lastname: Slater
authors.forename: Tomás
authors.initials: T
authors.lastname: Norambuena
authors.forename: Juan J
authors.initials: JJ
authors.lastname: Cifuentes
authors.forename: Leonardo I
authors.initials: LI
authors.lastname: Almonacid
authors.forename: Francisco
authors.initials: F
authors.lastname: Melo
mesh_terms: D000595:Amino Acid Sequence; D051777:AraC Transcription Factor / Q000737:chemistry / Q000145:classification*; D001665:Binding Sites; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D008958:Models, Molecular; D015233:Models, Statistical; D058977:Molecular Sequence Annotation / Q000379:methods*; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D014157:Transcription Factors / Q000737:chemistry / Q000145:classification*
chemical_list: D051777:AraC Transcription Factor; D014157:Transcription Factors