Kosaka Hiromichi, Hoseki Jun, Nakagawa Noriko, Kuramitsu Seiki, Masui Ryoji
Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan.
J Mol Biol. 2007 Nov 2;373(4):839-50. doi: 10.1016/j.jmb.2007.08.022. Epub 2007 Aug 21.
Uracil-DNA glycosylase (UDG) removes uracil generated by the deamination of cytosine or misincorporation of deoxyuridine monophosphate. Within the UDG superfamily, a fifth UDG family lacks a polar residue in the active-site motif, which mediates the hydrolysis of the glycosidic bond by activation of a water molecule in UDG families 1-4. We have determined the crystal structure of a novel family 5 UDG from Thermus thermophilus HB8 complexed with DNA containing an abasic site. The active-site structure suggests this enzyme uses both steric force and water activation for its excision reaction. A conserved asparagine residue acts as a ligand to the catalytic water molecule. The structure also implies that another water molecule acts as a barrier during substrate recognition. Based on no significant open-closed conformational change upon binding to DNA, we propose a "slide-in" mechanism for initial damage recognition.
尿嘧啶-DNA糖基化酶（UDG）可去除由胞嘧啶脱氨基或脱氧尿苷单磷酸错掺入产生的尿嘧啶。在UDG超家族中，第五个UDG家族在活性位点基序中缺乏一个极性残基，该残基在1-4家族的UDG中通过激活水分子介导糖苷键的水解。我们已经确定了嗜热栖热菌HB8中一个新的5型UDG与含有无碱基位点的DNA复合物的晶体结构。活性位点结构表明该酶在其切除反应中同时利用空间力和水激活。一个保守的天冬酰胺残基作为催化水分子的配体。该结构还表明另一个水分子在底物识别过程中起屏障作用。基于与DNA结合时没有明显的开闭构象变化，我们提出了一种“滑入”机制用于初始损伤识别。
