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Genes 2017, 8(1), 38; doi:10.3390/genes8010038

Sulfolobus acidocaldarius UDG Can Remove dU from the RNA Backbone: Insight into the Specific Recognition of Uracil Linked with Deoxyribose

State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
Author to whom correspondence should be addressed.
Academic Editor: Paolo Cinelli
Received: 27 November 2016 / Revised: 1 January 2017 / Accepted: 11 January 2017 / Published: 18 January 2017
(This article belongs to the Special Issue Replication and Transcription Associated DNA Repair)
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Sulfolobus acidocaldarius encodes family 4 and 5 uracil-DNA glycosylase (UDG). Two recombinant S. acidocaldarius UDGs (SacUDG) were prepared and biochemically characterized using oligonucleotides carrying a deaminated base. Both SacUDGs can remove deoxyuracil (dU) base from both double-stranded DNA and single-stranded DNA. Interestingly, they can remove U linked with deoxyribose from single-stranded RNA backbone, suggesting that the riboses on the backbone have less effect on the recognition of dU and hydrolysis of the C-N glycosidic bond. However, the removal of rU from DNA backbone is inefficient, suggesting strong steric hindrance comes from the 2′ hydroxyl of ribose linked to uracil. Both SacUDGs cannot remove 2,2′-anhydro uridine, hypoxanthine, and 7-deazaxanthine from single-stranded DNA and single-stranded DNA. Compared with the family 2 MUG, other family UDGs have an extra N-terminal structure consisting of about 50 residues. Removal of the 46 N-terminal residues of family 5 SacUDG resulted in only a 40% decrease in activity, indicating that the [4Fe-4S] cluster and truncated secondary structure are not the key elements in hydrolyzing the glycosidic bond. Combining our biochemical and structural results with those of other groups, we discussed the UDGs’ catalytic mechanism and the possible repair reactions of deaminated bases in prokaryotes. View Full-Text
Keywords: S. acidocaldarius; uracil-DNA glycosylase; [4Fe-4S] cluster; RNA backbone S. acidocaldarius; uracil-DNA glycosylase; [4Fe-4S] cluster; RNA backbone

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Yi, G.-S.; Wang, W.-W.; Cao, W.-G.; Wang, F.-P.; Liu, X.-P. Sulfolobus acidocaldarius UDG Can Remove dU from the RNA Backbone: Insight into the Specific Recognition of Uracil Linked with Deoxyribose. Genes 2017, 8, 38.

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