The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold
The catalytic domain of the P-type ATPase has the haloacid dehalogenase fold
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DOI：
10.1016/s0968-0004(98)01189-x
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发表时间：
1998-04-01
影响因子：
13.8
通讯作者：
Koonin, EV
中科院分区：
文献类型：
--
作者：
Aravind, L;Galperin, MY;Koonin, EV
P型ATP酶存在于生命的所有三个领域，并且已知在离子跨生物膜的运输中发挥关键作用1 -3。尽管P-型ATP酶的生理重要性和大量的生物化学研究，很少有人知道它们的结构功能关系和与其他酶家族的进化联系。序列比较有助于将利用ATP的酶分为几类不同的和古老的起源，如含有步行者基序的超家族，肌动蛋白糖激酶超家族和拓扑异构酶-组氨酸激酶超家族4 -6。这些超家族中的每一个都包括将磷酸转移到其他部分的磷酸转移酶和将生物学上有用的功与ATP水解的自由能偶联的ATP酶。在这里，我们表明，P-型ATP酶也属于水解酶的一个大的超家族，其结构上典型的L-2-卤酸脱卤酶（HAD）7，8从假单胞菌。这个超家族（以下简称HAD超家族）包括几个磷酸酶，并基于序列比较和底物结构，它似乎可能是P-型ATP酶共享一个共同的催化机制与这些酶。这一分析有助于预测P型ATP酶催化结构域的结构折叠，也为这一巨大类别的酶的进化历史提供了线索。当使用gapped BLAST程序9搜索国家生物技术信息中心的非冗余数据库时，P型ATP酶的蛋白质序列与来自其他家族的任何蛋白质没有显示统计学显著的相似性。然而，当使用PSI-BLAST程序迭代搜索时，其包括概况构建9，在6次迭代内检索到HAD超家族的许多蛋白质，期望（e）值在10-4至10-15的范围内。反过来，用HAD超家族的几个成员作为查询的搜索在三次迭代内检索e值范围从10-6到10-25的P型ATP酶。使用MoST程序10以严格的截止值（例如r= 0.0085）进行基序搜索产生相同的结果。在这些搜索中没有明显的假阳性，表明P型ATP酶确实属于HAD超家族。使用MACAW 11进一步比对序列，这导致在所有HAD超家族蛋白中描绘出三个统计学显著的基序（p~ 10-5至10-18）（图1）。
P-type ATPases are found in all three domains of life and are known to play a crucial role in the transport of ions across biological membranes1–3. In spite of the physiological importance of P-type ATPases and a number of extensive biochemical studies, little is known about their structure–function relationships and evolutionary connections with other enzyme families. Sequence comparisons have helped in the classification of ATP-utilizing enzymes into several classes of distinct and ancient origin, such as the Walker motif-containing superfamily, the actin-sugar kinase superfamily, and the topoisomerase-histidine kinase superfamily4–6. Each of these superfamilies includes phosphotransferases that transfer phosphate to other moieties and ATPases that couple biologically useful work with the free energy of ATP hydrolysis. Here we show that the P-type ATPases also belong to a large superfamily of hydrolases that are structurally typified by the L-2-haloacid dehalogenase (HAD) 7, 8 from Pseudomonas sp. This superfamily (hereinafter the HAD superfamily) includes several phosphatases, and based on sequence comparisons and the substrate structures, it seems likely that P-type ATPases share a common catalytic mechanism with these enzymes. This analysis helps in predicting the structural fold of the P-type ATPase catalytic domain and also provides clues to the evolutionary history of this vast class of enzymes. Protein sequences of P-type ATPases did not show statistically significant similarity to any proteins from other families when the non-redundant database at the National Center for Biotechnology Information was searched using the gapped BLAST program9. However, when the search was iterated using the PSI-BLAST program, which includes profile construction9, a number of proteins of the HAD superfamily were retrieved within six iterations with expectation (e) values in the range of 10–4 to 10–15. Reciprocally, searches with several members of the HAD superfamily used as queries retrieved P-type ATPases with e-values ranging from 10–6 to 10–25 within three iterations. Motif searches using the MoST program10 with stringent cutoffs (eg r= 0.0085) produced the same results. No false positives were apparent in any of these searches, indicating that P-type ATPases do, indeed, belong to the HAD superfamily. The sequences were further aligned using MACAW11, which resulted in the delineation of three statistically significant motifs (p~ 10–5 to 10–18) in all the HAD superfamily proteins (Fig. 1).