Structure of dNTP-inducible dNTP triphosphohydrolase: insight into broad specificity for dNTPs and triphosphohydrolase-type hydrolysis
Structure of dNTP-inducible dNTP triphosphohydrolase: insight into broad specificity for dNTPs and triphosphohydrolase-type hydrolysis
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DOI：
10.1107/s0907444906049262
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发表时间：
2007-02-01
期刊：
影响因子：
--
通讯作者：
Masui, Ryoji
中科院分区：
文献类型：
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作者：
Kondo, Naoyuki;Nakagawa, Noriko;Masui, Ryoji
嗜热栖热菌（Thermus thermophilus）的脱氧核苷三磷酸三磷酸水解酶（Tt-dNTPs）对脱氧核苷三磷酸（dNTPs）的降解具有独特的调控机制。而大肠杆菌同源物特异性水解dGTP单独，dNTPs作为底物和激活剂的Tt-dNTPs。在这里，Tt-dNTR的晶体结构已被确定在2.2埃分辨率，代表属于HD超家族的dNTR同源物的三级结构的第一份报告，不同的金属依赖性磷酸水解酶，包括各种未表征的蛋白质。这种酶形成一个同六聚体作为一个双环的三聚体。亚基由19个α-螺旋组成;内部6个螺旋包括注释为HD超家族的催化结构域的区域。与其他HD-超家族蛋白的结构比较表明，在中心的内部六个螺旋，形成高度保守的带电残基聚集在一个绑定的镁离子，口袋构成的催化位点。Tt-dNTR也水解非典型的dNTPs，但几乎不水解dNDP和dNMP。不同dNTP的广泛的底物特异性可能是合理的基础部分的分子识别过程中的一个灵活的环的参与。对活性至关重要的三磷酸部分的识别可以通过高度保守的带正电荷的残基来实现。根据结构讨论了dNTP结合的可能方式。
Deoxyribonucleoside triphosphate triphosphohydrolase from Thermus thermophilus (Tt-dNTPase) has a unique regulatory mechanism for the degradation of deoxyribonucleoside triphosphates (dNTPs). Whereas the Escherichia coli homologue specifically hydrolyzes dGTP alone, dNTPs act as both substrate and activator for Tt-dNTPase. Here, the crystal structure of Tt-dNTPase has been determined at 2.2 angstrom resolution, representing the first report of the tertiary structure of a dNTPase homologue belonging to the HD superfamily, a diverse group of metal-dependent phosphohydrolases that includes a variety of uncharacterized proteins. This enzyme forms a homohexamer as a double ring of trimers. The subunit is composed of 19 alpha-helices; the inner six helices include the region annotated as the catalytic domain of the HD superfamily. Structural comparison with other HD-superfamily proteins indicates that a pocket at the centre of the inner six helices, formed from highly conserved charged residues clustered around a bound magnesium ion, constitutes the catalytic site. Tt-dNTPase also hydrolyzed noncanonical dNTPs, but hardly hydrolyzed dNDP and dNMP. The broad substrate specificity for different dNTPs might be rationalized by the involvement of a flexible loop during molecular recognition of the base moiety. Recognition of the triphosphate moiety crucial for the activity might be attained by highly conserved positively charged residues. The possible mode of dNTP binding is discussed in light of the structure.