title: A new family of bacterial DNA repair proteins annotated by the integration of non-homology, distant homology and structural bioinformatic methods.
abstract: Different bioinformatics methods illuminate different aspects of protein function, from specific catalytic activities to broad functional categories. Here, a triple-pronged approach to predict function for a domain of unknown function, DUF2086, is applied. Distant homology to characterised enzymes and conservation of key residues suggest an oxygenase function. Modelling indicates that the substrate is most likely a nucleic acid. Finally, genomic context analysis linking DUF2086 to DNA repair, leads to a predicted activity of oxidative demethylation of damaged bases in DNA. The newly assigned activity is sporadically present in phyla not containing near relatives of the similarly active repair protein AlkB.
authors.affiliation: Structural and Chemical Biology, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
authors.forename: Luciane V
authors.initials: LV
authors.lastname: Mello
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Rigden
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D004249:DNA Damage; D004260:DNA Repair; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D007527:Isoenzymes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D006899:Mixed Function Oxygenases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D005810:Multigene Family; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D020592:Shewanella / Q000201:enzymology / Q000235:genetics*; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D007527:Isoenzymes; D006899:Mixed Function Oxygenases; C466427:AlkB protein, E coli