Base deamination is a common type of DNA damage that occurs in all organisms. DNA repair mechanisms are essential to maintain genome integrity, in which the base excision repair (BER) pathway plays a major role in the removal of base damage. In the BER pathway, the uracil DNA glycosylase superfamily is responsible for excising the deaminated bases from DNA and generates apurinic/apyrimidinic (AP) sites. Using bioinformatics tools, we identified a family 3 SMUG1-like DNA glycoyslase from Pedobacter heparinus (named Phe SMUG2), which displays catalytic activities towards DNA containing uracil or hypoxanthine/xanthine. Phylogenetic analyses show that SMUG2 enzymes are closely related to family 3 SMUG1s but belong to a distinct branch of the family. The high-resolution crystal structure of the apoenzyme reveals that the general fold of Phe SMUG2 resembles SMUG1s, yet with several distinct local structural differences. Mutational studies, coupled with structural modeling, identified several important amino acid residues for glycosylase activity. Substitution of G65 with a tyrosine results in loss of all glycosylase activity. The crystal structure of the G65Y mutant suggests a potential misalignment at the active site due to the mutation. The relationship between the new subfamily and other families in the UDG superfamily is discussed. The present study provides new mechanistic insight into the molecular mechanism of the UDG superfamily.
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Cover Image
Cover Image
The interfacial active site of the type IB GTP cyclohydrolase from Neisseria gonorrhoeae (grey and green ribbons), in complex with zinc (magenta ball) and the reaction intermediate analog and potent inhibitor 8-oxo-GTP (stick model). The structure sheds light on the complex and unique catalytic strategy of this potential antibacterial target, and offers a starting point for the design of specific inhibitors against the enzyme. For more information, please see study by Paranagama et al. in this issue, pages 1017–1039. Image provided by Manal Swairjo.
SMUG2 DNA glycosylase from Pedobacter heparinus as a new subfamily of the UDG superfamily
Panjiao Pang, Ye Yang, Jing Li, Zhong Wang, Weiguo Cao, Wei Xie; SMUG2 DNA glycosylase from Pedobacter heparinus as a new subfamily of the UDG superfamily. Biochem J 15 March 2017; 474 (6): 923–938. doi: https://doi.org/10.1042/BCJ20160934
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