The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features
The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features
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DOI：
10.1107/s0907444903011144
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发表时间：
2003-08-01
影响因子：
2.2
通讯作者：
Willassen, NP
中科院分区：
文献类型：
--
作者：
Leiros, I;Moe, E;Willassen, NP
尿嘧啶-DNA 糖基化酶（UDG；EC 3.2.2.3）是一种 DNA 修复蛋白，可催化单链或双链 DNA 中促诱变尿嘧啶残基的水解，产生游离尿嘧啶和脱碱基 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为 1.9 埃分辨率，工作反射集和测试集反射的最终 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糖基化酶的第一个晶体结构，并且与人类酶进行了详细比较，以便在结构水平上合理化鳕鱼酶的冷适应行为。 cUDG的催化结构域包含223个残基，与人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埃。对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进行比较和讨论，以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灵活性和/或稳定性。与 hUDG 相比，cUDG 面向 DNA 一侧的正静电表面电位增加似乎是增加对带负电 DNA 的亲和力的原因。
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 Angstrom 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 Angstrom. 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.