Leiros Ingar, Moe Elin, Lanes Olav, Smalås Arne O, Willassen Nils P
Department of Chemistry, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway.
Acta Crystallogr D Biol Crystallogr. 2003 Aug;59(Pt 8):1357-65. doi: 10.1107/s0907444903011144. Epub 2003 Jul 23.
Uracil-DNA glycosylase (UDG; EC 3.2.2.3) is a DNA-repair protein that catalyses the hydrolysis of promutagenic uracil residues from single- or double-stranded DNA, generating free uracil and abasic DNA. The crystal structure of the catalytic domain of cod uracil-DNA glycosylase (cUDG) has been determined to 1.9 A resolution, with final R factors of 18.61 and 20.57% for the working and test sets of reflections, respectively. This is the first crystal structure of a uracil-DNA glycosylase from a cold-adapted species and a detailed comparison with the human enzyme is performed in order to rationalize the cold-adapted behaviour of the cod enzyme at the structural level. The catalytic domain of cUDG comprises 223 residues, with a sequence identity to the human UDG of 75%. The tertiary structures of the two enzymes are also similar, with an overall displacement in main-chain atomic positions of 0.63 A. The amino-acid substitutions and the differences in intramolecular hydrogen bonds, hydrophobic interactions, ion-pair interactions and electrostatic potentials are compared and discussed in order to gain insight into the factors that cause the increased activity and reduced thermostability of the cod enzyme. In particular, the reduced number of strong ion-pair interactions in the C-terminal half of cUDG is believed to greatly affect the flexibility and/or stability. Increased positive electrostatic surface potential on the DNA-facing side of cUDG seems to be responsible for increasing the affinity for the negatively charged DNA compared with that of hUDG.
尿嘧啶-DNA糖基化酶（UDG；EC 3.2.2.3）是一种DNA修复蛋白，它催化从单链或双链DNA中水解诱变前体尿嘧啶残基，生成游离尿嘧啶和无碱基DNA。鳕鱼尿嘧啶-DNA糖基化酶（cUDG）催化结构域的晶体结构已确定分辨率为1.9 Å，工作和测试反射集的最终R因子分别为18.61%和20.57%。这是来自冷适应物种的尿嘧啶-DNA糖基化酶的首个晶体结构，并与人类酶进行了详细比较，以便在结构水平上解释鳕鱼酶的冷适应行为。cUDG的催化结构域由223个残基组成，与人类UDG的序列同一性为75%。两种酶的三级结构也相似，主链原子位置的总体位移为0.63 Å。比较并讨论了氨基酸取代以及分子内氢键、疏水相互作用、离子对相互作用和静电势的差异，以便深入了解导致鳕鱼酶活性增加和热稳定性降低的因素。特别是，cUDG C端一半中强离子对相互作用数量的减少被认为极大地影响了其灵活性和/或稳定性。与hUDG相比，cUDG面向DNA一侧增加的正静电表面电位似乎是其对带负电荷的DNA亲和力增加的原因。
