title: Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity.
abstract: Repair of uracils in DNA is initiated by uracil DNA glycosylases (UDGs). Family 1 UDGs (Ung) are the most efficient and ubiquitous proteins having an exquisite specificity for uracils in DNA. Ung are characterized by motifs A (GQDPY) and B (HPSPLS) sequences. We report a novel dimeric UDG, Blr0248 (BdiUng) from Bradyrhizobium diazoefficiens. Although BdiUng contains the motif A (GQDPA), it has low sequence identity to known UDGs. BdiUng prefers single stranded DNA and excises uracil, 5-hydroxymethyl-uracil or xanthine from it. BdiUng is impervious to inhibition by AP DNA, and Ugi protein that specifically inhibits family 1 UDGs. Crystal structure of BdiUng shows similarity with the family 4 UDGs in its overall fold but with family 1 UDGs in key active site residues. However, instead of a classical motif B, BdiUng has a uniquely extended protrusion explaining the lack of Ugi inhibition. Structural and mutational analyses of BdiUng have revealed the basis for the accommodation of diverse substrates into its substrate binding pocket. Phylogenetically, BdiUng belongs to a new UDG family. Bradyrhizobium diazoefficiens presents a unique scenario where the presence of at least four families of UDGs may compensate for the absence of an efficient family 1 homologue.
authors.affiliation: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.
authors.forename: Ullas Valiya
authors.initials: UV
authors.lastname: Chembazhi
authors.affiliation: Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-Ro, Yuseon-Gu, Daejeon 34141, Republic of Korea.|Department of Bio-Analytical Science, University of Science and Technology, Daejeon 34113, Republic of Korea.
authors.forename: Vinod Vikas
authors.initials: VV
authors.lastname: Patil
authors.affiliation: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.
authors.forename: Shivjee
authors.initials: S
authors.lastname: Sah
authors.affiliation: Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia.
authors.forename: Wayne
authors.initials: W
authors.lastname: Reeve
authors.affiliation: Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia.
authors.forename: Ravi P
authors.initials: RP
authors.lastname: Tiwari
authors.affiliation: Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-Ro, Yuseon-Gu, Daejeon 34141, Republic of Korea.|Department of Bio-Analytical Science, University of Science and Technology, Daejeon 34113, Republic of Korea.
authors.forename: Euijeon
authors.initials: E
authors.lastname: Woo
authors.affiliation: Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.|Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150, Australia.|Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.
authors.forename: Umesh
authors.initials: U
authors.lastname: Varshney
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D020369:Bradyrhizobium / Q000201:enzymology* / Q000235:genetics; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D004249:DNA Damage; D004260:DNA Repair; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D007700:Kinetics; D008958:Models, Molecular; D009154:Mutation; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D055503:Protein Multimerization; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity; D014498:Uracil / Q000378:metabolism*; D051981:Uracil-DNA Glycosidase / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004277:DNA, Single-Stranded; D011994:Recombinant Proteins; D014498:Uracil; D051981:Uracil-DNA Glycosidase