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GDP-甘露糖糖基水解酶的结构与机制，一种在碳原子而非磷原子处进行切割的Nudix酶。

Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus.

作者信息

Gabelli Sandra B, Bianchet Mario A, Azurmendi Hugo F, Xia Zuyong, Sarawat Vibhor, Mildvan Albert S, Amzel L Mario

机构信息

Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA.

出版信息

Structure. 2004 Jun;12(6):927-35. doi: 10.1016/j.str.2004.03.028.

DOI:10.1016/j.str.2004.03.028

PMID:15274914

Abstract

GDP-mannose glycosyl hydrolase (GDPMH) catalyzes the hydrolysis of GDP-mannose and GDP-glucose to GDP and sugar by substitution with inversion at C1 of the sugar. The enzyme has a modified Nudix motif and requires one divalent cation for activity. The 1.3 A X-ray structure of the GDPMH-Mg(2+)-GDP complex, together with kinetic, mutational, and NMR data, suggests a mechanism for the GDPMH reaction. Several residues and the divalent cation strongly promote the departure of the GDP leaving group, supporting a dissociative mechanism. Comparison of the GDPMH structure with that of a typical Nudix hydrolase suggests how sequence changes result in the switch of catalytic activity from P-O bond cleavage to C-O bond cleavage. Changes in the Nudix motif result in loss of binding of at least one Mg(2+) ion, and shortening of a loop by 6 residues shifts the catalytic base by approximately 10 A.

摘要

GDP-甘露糖糖基水解酶（GDPMH）通过在糖的C1位进行取代并伴随构型翻转，催化GDP-甘露糖和GDP-葡萄糖水解为GDP和糖。该酶具有一个修饰的Nudix基序，并且活性需要一个二价阳离子。GDPMH-Mg(2+)-GDP复合物的1.3埃X射线结构，连同动力学、突变和核磁共振数据，提示了GDPMH反应的一种机制。几个残基和二价阳离子强烈促进GDP离去基团的离去，支持一种解离机制。将GDPMH结构与典型的Nudix水解酶结构进行比较，揭示了序列变化如何导致催化活性从P-O键断裂转变为C-O键断裂。Nudix基序的变化导致至少一个Mg(2+)离子结合的丧失，并且一个环缩短6个残基使催化碱基移动了约10埃。