title: SMUG2 DNA glycosylase fromPedobacter heparinusas a new subfamily of the UDG superfamily.
abstract: 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 fromPedobacter 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.
authors.affiliation: School of Pharmaceutical Sciences, The Sun Yat-Sen University, 132 E. Circle Rd. University City, Guangzhou, Guangdong 510006, People's Republic of China.
authors.forename: Panjiao
authors.initials: P
authors.lastname: Pang
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, 190 Collings Street, Clemson, SC 29634, U.S.A.
authors.forename: Ye
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, 190 Collings Street, Clemson, SC 29634, U.S.A.
authors.forename: Jing
authors.initials: J
authors.lastname: Li
authors.affiliation: School of Pharmaceutical Sciences, The Sun Yat-Sen University, 132 E. Circle Rd. University City, Guangzhou, Guangdong 510006, People's Republic of China.
authors.forename: Zhong
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, 190 Collings Street, Clemson, SC 29634, U.S.A.
authors.forename: Weiguo
authors.initials: W
authors.lastname: Cao
authors.affiliation: State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, 135 W. Xingang Rd., Guangzhou, Guangdong 510275, People's Republic of China wgc@clemson.edu xiewei6@mail.sysu.edu.cn.
authors.forename: Wei
authors.initials: W
authors.lastname: Xie
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004249:DNA Damage; D004260:DNA Repair; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D005998:Glycine / Q000737:chemistry / Q000378:metabolism; D007527:Isoenzymes / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D005810:Multigene Family; D009154:Mutation; D060485:Pedobacter / Q000145:classification / Q000201:enzymology* / Q000235:genetics; D010802:Phylogeny; D011485:Protein Binding; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity; D014443:Tyrosine / Q000737:chemistry / Q000378:metabolism; D051981:Uracil-DNA Glycosidase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D007527:Isoenzymes; D011994:Recombinant Proteins; D014443:Tyrosine; D051981:Uracil-DNA Glycosidase; D005998:Glycine