Structural basis for nucleotide binding and reaction catalysis in mevalonate diphosphate decarboxylase.
Structural basis for nucleotide binding and reaction catalysis in mevalonate diphosphate decarboxylase.
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DOI：
10.1021/bi300591x
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发表时间：
2012-07-17
期刊：
影响因子：
2.9
通讯作者：
Geisbrecht BV
中科院分区：
文献类型：
--
作者：
Barta ML;McWhorter WJ;Miziorko HM;Geisbrecht BV
甲氧丙酮二磷酸脱羧酶(MDD)催化甲氧戊酸途径的最后一步，即依赖于镁离子-三磷酸腺苷的甲戊酸5-二磷酸(MVAPP)的脱羧基，生成异戊烯基二磷酸(IPP)。IPP是一种类异戊二烯前体分子，是肽聚糖和类异戊二烯生物合成的关键中间体，在革兰氏阳性菌(如葡萄球菌、链球菌和肠球菌)的合成中是必不可少的。因此，甲氧丙酮酸途径的酶是理想的抗菌靶点。MDD是近50年来被广泛研究的GHMP小分子(即代谢物)激酶超家族，但其三元复合体的结晶一直比较困难。为了进一步了解GHMP激酶的催化机制，以开发针对底物和核苷酸结合位点的广谱抗菌剂，我们报道了表皮葡萄球菌MDD野生型和突变型(S192A和D283A)三元复合体的晶体结构。比较apo、MVAPP结合和三元络合野生型MDD提供了底物结合模式和催化机制的结构信息。对催化缺陷型MDD S192A和D283A的三元络合物(kcat分别降低103倍和105倍)的结构表征提供了对MDD功能的洞察。不变Asp283的羧酸侧链起催化碱的作用，对于MVAPP C3-羟基在活性中心漏斗中的正确定位是必不可少的。保守的磷酸结合环(‘P-loop’)中的几个MDD氨基酸提供了关键的相互作用，稳定了核苷酸的三磷酰基部分。这些晶体结构为基于结构的药物设计提供了有用的基础。
Mevalonate diphosphate decarboxylase (MDD) catalyzes the final step of the mevalonate pathway, the Mg++-ATP dependent decarboxylation of mevalonate 5-diphosphate (MVAPP), producing isopentenyl diphosphate (IPP). Synthesis of IPP, an isoprenoid precursor molecule that is a critical intermediate in peptidoglycan and polyisoprenoid biosynthesis, is essential in Gram-positive bacteria (e.g. Staphylococcus, Streptococcus and Enterococcus spp.) and thus the enzymes of the mevalonate pathway are ideal antimicrobial targets. MDD belongs to the GHMP superfamily of small molecule (i.e. metabolite) kinases that have been extensively studied for the past 50 years, yet the crystallization of GHMP kinase ternary complexes has proven difficult. To further our understanding of the catalytic mechanism of GHMP kinases with the purpose of developing broad spectrum antimicrobial agents that target the substrate and nucleotide binding sites, we report the crystal structures of wild-type and mutant (S192A and D283A) ternary complexes of Staphylococcus epidermidis MDD. Comparison of apo-, MVAPP-bound and ternary complexed wild-type MDD provides structural information on the mode of substrate binding and the catalytic mechanism. Structural characterization of ternary complexes of catalytically deficient MDD S192A and D283A (decreased kcat of 103-fold and 105-fold, respectively) provides insight into MDD function. The carboxylate side chain of invariant Asp283 functions as a catalytic base and is essential to the proper orientation of the MVAPP C3-hydroxyl group within the active site funnel. Several MDD amino acids within the conserved phosphate binding loop (‘P-loop’) provide key interactions, stabilizing the nucleotide triphosphoryl moiety. The crystal structures presented here provide a useful foundation for structure-based drug design.
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DOI：
10.1016/0167-4838(87)90170-1
发表时间：
1987-12-18
期刊：
BIOCHIMICA ET BIOPHYSICA ACTA
影响因子：
--
作者：
CHIEW, YE;OSULLIVAN, WJ;LEE, CS
通讯作者：
LEE, CS
影响因子：
2.9
作者：
Andreassi, John L., II;Vetting, Matthew W.;Bilder, Patrick W.;Roderick, Steven L.;Leyh, Thomas S.
通讯作者：
Leyh, Thomas S.
影响因子：
5.8
作者：
Gouet, P;Courcelle, E;Métoz, F
通讯作者：
Métoz, F
DOI：
10.1107/s0907444904019158
发表时间：
2004-12-01
影响因子：
2.2
作者：
Emsley, P;Cowtan, K
通讯作者：
Cowtan, K
影响因子：
4.8
作者：
Barta, Michael L.;Skaff, D. Andrew;Geisbrecht, Brian V.
通讯作者：
Geisbrecht, Brian V.