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

• Ullas Valiya Chembazhi ^[3] ; Vinod Vikas Patil ^[1] ; Shivjee Sah ^[3] ; Wayne Reeve ^[2] ; Ravi P. Tiwari ^[2] ; Euijeon Woo ^[1] ; Umesh Varshney ^[4]
  1. [1] Korea Research Institute of Bioscience and Biotechnology

     Korea Research Institute of Bioscience and Biotechnology

     Corea del Sur

     
  2. [2] Murdoch University

     Murdoch University

     Australia

     
  3. [3] Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
  4. [4] 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

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• Localización: Nucleic acids research, ISSN 0305-1048, Vol. 45, Nº. 10, 2017, págs. 5863-5876
• Idioma: inglés
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  • 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.