5GRK

Crystal structure of Uracil DNA glycosylase -Xanthine complex from Bradyrhizobium diazoefficiens

5GRK の概要

• エントリーDOI: 10.2210/pdb5grk/pdb
• 関連するPDBエントリー: 5GN2 5GN3 5GNW
• 分子名称: Blr0248 protein, XANTHINE (2 entities in total)
• 機能のキーワード: uracil dna glycosylase (udg) bradyrhizobium diazoefficiens, nitrogen fixing symbiont, dna repair, xanthine., hydrolase
• 由来する生物種: Bradyrhizobium diazoefficiens USDA 110
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 119511.62

構造登録者

Patil, V.V.,Ullas, V.C.,Ahn, W.,Varshney, U.,Woo, E. (登録日: 2016-08-11, 公開日: 2017-05-03, 最終更新日: 2017-06-14)

主引用文献

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

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: 28369586
DOI: 10.1093/nar/gkx209

実験手法

X-RAY DIFFRACTION (2.804 Å)