Phosphoesterase domains associated with DNA polymerases of diverse origins
Phosphoesterase domains associated with DNA polymerases of diverse origins
复制标题
DOI：
10.1093/nar/26.16.3746
复制
发表时间：
1998-08-15
影响因子：
14.9
通讯作者：
Koonin, EV
中科院分区：
文献类型：
--
作者：
Aravind, L;Koonin, EV
DMA聚合酶蛋白质序列的计算机分析显示，以前未确定的保守结构域属于两个不同的超家族的磷酸酯酶。细菌DNA聚合酶III和两个不同的X家族DNA聚合酶的α亚基被证明含有一个N-末端结构域，该结构域定义了一个新的酶超家族，命名为PHP，聚合酶和组氨醇磷酸酶后。预测的PHP超家族的催化位点由四个基序组成，这些基序含有保守的组氨酸残基，这些残基可能参与磷酸酯键水解的金属依赖性催化。PHP结构域在所有细菌聚合酶III α亚基中是高度保守的，但在变形菌和支原体中，保守的基序被扭曲，表明酶活性的丧失。在古细菌DNA聚合酶II和真核生物DNA聚合酶α和δ的小亚基中发现的另一个保守结构域被证明属于钙调神经磷酸酶样磷酸酯酶超家族，其联合多种磷酸酶和核酸酶。磷酸酯酶活性所需的保守基序在古细菌DNA聚合酶亚基中是完整的，但在其真核生物直向同源物中被破坏。提出了一个假设，细菌和古细菌复制型DNA聚合酶具有内在的磷酸酶活性，水解核苷酸聚合过程中释放的焦磷酸盐。如前所述，焦磷酸水解可能是驱动聚合反应向前发展所必需的。具有破坏的催化基序的磷酸酯酶结构域可以承担变构的调节功能和/或结合DNA聚合酶全酶的其他亚基。在这些情况下，焦磷酸盐可以被独立的磷酸酶水解，并且在细菌PHP超家族成员中鉴定了这种作用的候选者。
Computer analysis of DMA polymerase protein sequences revealed previously unidentified conserved domains that belong to two distinct superfamilies of phosphoesterases. The alpha subunits of bacterial DNA polymerase III and two distinct family X DNA polymerases are shown to contain an N-terminal domain that defines a novel enzymatic superfamily, designated PHP, after polymerase and histidinol phosphatase. The predicted catalytic site of the PHP superfamily consists of four motifs containing conserved histidine residues that are likely to be Involved in metal-dependent catalysis of phosphoester bond hydrolysis. The PHP domain is highly conserved in all bacterial polymerase ill alpha subunits, but in proteobacteria and mycoplasmas, the conserved motifs are distorted, suggesting a loss of the enzymatic activity. Another conserved domain, found in the small subunits of archaeal DNA polymerase II and eukaryotic DNA polymerases alpha and delta, is shown to belong to-the superfamily of calcineurin-like phosphoesterases, which unites a variety of phosphatases and nucleases, The conserved motifs required for phosphoesterase activity are intact in the archaeal DNA polymerase subunits, but are disrupted in their eukaryotic orthologs. A hypothesis is proposed that bacterial and archaeal replicative DNA polymerases possess intrinsic phosphatase activity that hydrolyzes the pyrophosphate released during nucleotide polymerization. As proposed previously, pyrophosphate hydrolysis may be necessary to drive the polymerization reaction forward, The phosphoesterase domains with disrupted catalytic motifs may assume an allosteric, regulatory function and/or bind other subunits of DNA polymerase holoenzymes. In these cases, the pyrophosphate may be hydrolyzed by a stand-alone phosphatase, and candidates for such a role were identified among bacterial PHP superfamily members.