Structure of the ternary complex of phosphomevalonate kinase: the enzyme and its family.
Structure of the ternary complex of phosphomevalonate kinase: the enzyme and its family.
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DOI：
10.1021/bi900537u
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发表时间：
2009-07-14
期刊：
影响因子：
2.9
通讯作者：
Leyh, Thomas S.
中科院分区：
文献类型：
--
作者：
Andreassi, John L., II;Vetting, Matthew W.;Bilder, Patrick W.;Roderick, Steven L.;Leyh, Thomas S.
半乳糖基、高丝氨酸、甲氧丙戊酸、磷酸戊酸-激酶(GHMP)超家族具有广泛的蛋白质功能。该家族的三个成员(甲氧丙戊酸激酶、磷酸丙戊酸激酶和二磷酸丙戊酸脱羧酶)构成了在肺炎链球菌和其他生物中发现的甲氧丙酮酸途径。我们测定了肺炎链球菌磷酸戊酸激酶(PMK)与磷酸戊酸和AMPPNP·Mg~(2+)的络合物的晶体结构。对apo和三元pMK结构的比较表明，配体结合颠倒了两个反平行赖氨酸残基(100和101)的侧链方向，结果是lys101“切换”到其氨离子与核苷酸的β，γ桥原子直接接触的位置，在那里它有望稳定反应的基态和过渡态。对所有可用的GHMP激酶三元复合体结构的分析表明，虽然它们的Cα支架高度保守，但它们的底物以两种构象中的一种结合，看起来要么是反应性的，要么是非反应性的。PMK的活性中心似乎足够大，以适应反应性和非反应性构象的相互转化。PMK活性中心的很大一部分被有序的水占据，这些有序水聚集在衬底的带电区域附近。值得注意的是，在活性部位发现了与两种底物的活性基团广泛相互作用的水五聚体。
The Galacto-, Homoserine-, Mevalonate-, Phosphomevalonate-kinase (GHMP) superfamily encompases a wide-range of protein function. Three members of the family (mevalonate kinase, phosphomevalonate kinase and diphosphomevalonate decarboxylase) comprise the mevalonate pathway found in S. pneumoniae and other organisms. We have determined the 1.9 Å crystal structure of phosphomevalonate kinase (PMK) from S. pneumoniae in complex with phosphomevalonate and AMPPNP·Mg2+. Comparison of the apo and ternary PMK structures suggests that ligand binding reverses the side-chain orientations of two anti-parallel lysines residues (100 and 101) with the result that lys101 is “switched” into a position in which its ammonium ion is in direct contact with the β,γ-bridging atom of the nucleotide, where it is expected to stabilize both the ground and transition states of the reaction. Analysis of all available GHMP kinase ternary-complex structures reveals that while their Cα-scaffolds are highly conserved, their substrates bind in one of two conformations, which appear to be either reactive or non-reactive. The active site of PMK seems spacious enough to accommodate interconversion of the reactive and nonreactive conformers. A substantial fraction of the PMK active site is occupied by ordered water, which clusters near the charged regions of substrate. Notably, a water pentamer that interacts extensively with the reactive groups of both substrates was discovered at the active site.
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影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium
DOI：
10.1107/s0907444901012458
发表时间：
2001-10-01
影响因子：
2.2
作者：
Kissinger, CR;Gehlhaar, DK;Bouzida, D
通讯作者：
Bouzida, D
影响因子：
2.9
作者：
Andreassi, JL;Dabovic, K;Leyh, TS
通讯作者：
Leyh, TS
影响因子：
2.9
作者：
Krishna, SS;Zhou, T;Zhang, H
通讯作者：
Zhang, H
影响因子：
2.9
作者：
Harker, HA;Viant, MR;Saykally, RJ
通讯作者：
Saykally, RJ