Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity

U.V. Chembazhi; V.V. Patil; S. Sah; W. Reeve; R.P. Tiwari; E. Woo; U. Varshney

doi:10.1093/nar/gkx209

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Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity

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Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity

U.V. Chembazhi, V.V. Patil, S. Sah, W. Reeve, R.P. Tiwari, E. Woo and U. Varshney

Nucleic Acids Research, Vol.45(10), pp.5863-5876

2017

DOI: https://doi.org/10.1093/nar/gkx209

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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.

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Title: Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity
Authors/Creators: U.V. Chembazhi (Author/Creator) - Indian Institute of Science Bangalore
V.V. Patil (Author/Creator) - Korea University of Science and Technology
S. Sah (Author/Creator) - Indian Institute of Science Bangalore
W. Reeve (Author/Creator) - Murdoch University
R.P. Tiwari (Author/Creator) - Murdoch University
E. Woo (Author/Creator) - Korea University of Science and Technology
U. Varshney (Author/Creator) - Murdoch University
Publication Details: Nucleic Acids Research, Vol.45(10), pp.5863-5876
Publisher: Oxford University Press
Identifiers: 991005542178907891
Copyright: © 2017 Oxford University Press
Murdoch Affiliation: School of Veterinary and Life Sciences; Centre for Rhizobium Studies
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.152 Molecular & Cell Biology - DNA Damage; 1.152.251 Nucleotide Excision Repair
Web Of Science research areas: Biochemistry & Molecular Biology
ESI research areas: Biology & Biochemistry