Chembazhi Ullas Valiya, Patil Vinod Vikas, Sah Shivjee, Reeve Wayne, Tiwari Ravi P, Woo Euijeon, Varshney Umesh
Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India.
Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-Ro, Yuseon-Gu, Daejeon 34141, Republic of Korea.
Nucleic Acids Res. 2017 Jun 2;45(10):5863-5876. doi: 10.1093/nar/gkx209.
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.
DNA中尿嘧啶的修复由尿嘧啶DNA糖基化酶（UDGs）启动。1型UDGs（Ung）是最有效且分布最广泛的蛋白质，对DNA中的尿嘧啶具有极高的特异性。Ung的特征在于基序A（GQDPY）和B（HPSPLS）序列。我们报道了一种来自慢生根瘤菌的新型二聚体UDG，即Blr0248（BdiUng）。尽管BdiUng含有基序A（GQDPA），但它与已知的UDGs序列同一性较低。BdiUng更喜欢单链DNA，并从中切除尿嘧啶、5-羟甲基尿嘧啶或黄嘌呤。BdiUng不受AP DNA和特异性抑制1型UDGs的Ugi蛋白的抑制。BdiUng的晶体结构在整体折叠上与4型UDGs相似，但在关键活性位点残基上与1型UDGs相似。然而，BdiUng没有经典的基序B，而是有一个独特的延伸突出结构，这解释了它不受Ugi抑制的原因。对BdiUng的结构和突变分析揭示了其底物结合口袋容纳多种底物的基础。从系统发育角度来看，BdiUng属于一个新的UDG家族。慢生根瘤菌呈现出一种独特的情况，即至少四个UDG家族的存在可能弥补了高效1型同源物的缺失。
