5GN3
Structure of selenomethionine-labelled Uracil DNA glycosylase (BdiUNG) from Bradyrhizobium diazoefficiens
Summary for 5GN3
| Entry DOI | 10.2210/pdb5gn3/pdb |
| Related | 5GN2 5GNW 5GRK |
| Descriptor | Blr0248 protein (2 entities in total) |
| Functional Keywords | uracil dna glycosylase (udg), bradyrhizobium diazoefficiens, nitrogen fixing symbiont, hydrolase |
| Biological source | Bradyrhizobium diazoefficiens USDA 110 |
| Total number of polymer chains | 4 |
| Total formula weight | 119841.08 |
| Authors | Patil, V.V.,Chembazhi, U.V.,Varshney, U.,Woo, E. (deposition date: 2016-07-19, release date: 2017-05-03, Last modification date: 2024-11-13) |
| Primary citation | Chembazhi, U.V.,Patil, V.V.,Sah, S.,Reeve, W.,Tiwari, R.P.,Woo, E.,Varshney, U. Uracil DNA glycosylase (UDG) activities in Bradyrhizobium diazoefficiens: characterization of a new class of UDG with broad substrate specificity Nucleic Acids Res., 45:5863-5876, 2017 Cited by PubMed 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. PubMed: 28369586DOI: 10.1093/nar/gkx209 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.281 Å) |
Structure validation
Download full validation report
