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A new family of bacterial DNA repair proteins annotated by the integration of non-homology, distant homology and structural bioinformatic methods

A new family of bacterial DNA repair proteins annotated by the integration of non-homology, distant homology and structural bioinformatic methods

Febs Letters 586(21): 3908-3913

ISSN/ISBN: 0014-5793

PMID: 23022560

DOI: 10.1016/j.febslet.2012.09.023

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.

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Accession: 036593457

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