Bacillus subtilis YkuK protein is distantly related to RNase H |
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Authors: | Knizewski Łukasz Ginalski Krzysztof |
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Institution: | Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Pawińskiego 5A, 02-106 Warsaw, Poland. |
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Abstract: | In addition to one hypothetical viral sequence from Bacteriophage KVP40, the PfamA family of unknown function DUF458 (Pfam Accession No. PF04308) encompasses several uncharacterized bacterial proteins including Bacillus subtilis YkuK protein. Using Meta-BASIC, a highly sensitive method for detection of distant similarity between proteins, we assign DUF458 family members to the ribonuclease H-like (RNase H-like) superfamily. DUF458 sequences maintain all core secondary structure elements of RNase H-like fold and share several conserved, presumably active site residues with RNase HI, including an invariant DDE motif. In addition to providing a model structure for a previously uncharacterized protein family, this finding suggests that DUF458 proteins function as nucleases. The unusual phyletic pattern, together with a presence of DUF458 in several thermophilic organisms, may suggest a potential role of these proteins in DNA repair in stressful conditions such as an extreme heat or other stress that causes spore formation. |
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Keywords: | YkuK DUF458 family RNase H-like fold Structure/function prediction Active site Nuclease |
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