Crystal Structures of Staphylococcus epidermidis Mevalonate Diphosphate Decarboxylase Bound to Inhibitory Analogs Reveal New Insight into Substrate Binding and Catalysis
Crystal Structures of Staphylococcus epidermidis Mevalonate Diphosphate Decarboxylase Bound to Inhibitory Analogs Reveal New Insight into Substrate Binding and Catalysis
复制标题
DOI：
10.1074/jbc.m111.242016
复制
发表时间：
2011-07-08
影响因子：
4.8
通讯作者：
Geisbrecht, Brian V.
中科院分区：
文献类型：
--
作者：
Barta, Michael L.;Skaff, D. Andrew;Geisbrecht, Brian V.
聚类异戊二烯化合物磷酸十一异戊二烯酯是革兰氏阳性细菌（包括致病性肠球菌、链球菌和葡萄球菌属）中细胞壁肽聚糖生物合成所需的。在这些生物体中，甲羟戊酸途径用于产生前体类异戊二烯，异戊烯基5-二磷酸。甲羟戊酸二磷酸脱羧酶（MDD）催化异戊烯基5-二磷酸在ATP依赖性不可逆反应中的形成，因此是抑制剂开发的有吸引力的靶点，可能导致新的抗微生物剂。为了便于探索这种可能性，我们报告了表皮葡萄球菌MDD的晶体结构（1.85埃分辨率），并据我们所知，配体MDD的第一个结构。这些结构包括与甲羟戊酸5-二磷酸类似物二磷酸羟乙酰脯氨酸（2.05埃分辨率）和6-氟甲羟戊酸二磷酸（FMVAPP; 2.2埃分辨率）结合的MDD。这些结构的比较为这些抑制剂观察到的Ki值的显著差异提供了物理基础。对酶/抑制剂结构的检查确定了不变Ser（192）的侧链对催化作用有潜在的贡献。值得注意的是，该侧链的Ser -> Ala取代使k（cat）降低了约10（3）倍，即使FMVAPP和该突变体之间的结合相互作用与野生型MDD观察到的类似，如通过S192 A与FMVAPP的2.1埃共晶结构所判断的。微生物MDD结构与哺乳动物对应物的比较揭示了活性位点外围的潜在靶点，这些靶点可用于选择性靶向微生物酶。这些研究为以前关于MDD机制的观察提供了结构基础，并为未来合理的抑制剂设计提供了信息。
The polyisoprenoid compound undecaprenyl phosphate is required for biosynthesis of cell wall peptidoglycans in Gram-positive bacteria, including pathogenic Enterococcus, Streptococcus, and Staphylococcus spp. In these organisms, the mevalonate pathway is used to produce the precursor isoprenoid, isopentenyl 5-diphosphate. Mevalonate diphosphate decarboxylase (MDD) catalyzes formation of isopentenyl 5-diphosphate in an ATP-dependent irreversible reaction and is therefore an attractive target for inhibitor development that could lead to new antimicrobial agents. To facilitate exploration of this possibility, we report the crystal structure of Staphylococcus epidermidis MDD (1.85 angstrom resolution) and, to the best of our knowledge, the first structures of liganded MDD. These structures include MDD bound to the mevalonate 5-diphosphate analogs diphosphoglycolyl proline (2.05 angstrom resolution) and 6-fluoromevalonate diphosphate (FMVAPP; 2.2 angstrom resolution). Comparison of these structures provides a physical basis for the significant differences in K-i values observed for these inhibitors. Inspection of enzyme/inhibitor structures identified the side chain of invariant Ser(192) as making potential contributions to catalysis. Significantly, Ser -> Ala substitution of this side chain decreases k(cat) by similar to 10(3)-fold, even though binding interactions between FMVAPP and this mutant are similar to those observed with wild type MDD, as judged by the 2.1 angstrom cocrystal structure of S192A with FMVAPP. Comparison of microbial MDD structures with those of mammalian counterparts reveals potential targets at the active site periphery that may be exploited to selectively target the microbial enzymes. These studies provide a structural basis for previous observations regarding the MDD mechanism and inform future work toward rational inhibitor design.