Crystal structure of the C67A mutant of isopentenyl diphosphate isomerase complexed with a mechanism-based irreversible inhibitor

• Published in: Proteins, structure, function, and bioinformatics Vol. 54; no. 2; pp. 216 - 221
• Main Authors: Wouters, J., Oudjama, Y., Stalon, V., Droogmans, L., Poulter, C.D.
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01.02.2004
• Subjects: Binding Sites; Carbon-Carbon Double Bond Isomerases - antagonists & inhibitors; Carbon-Carbon Double Bond Isomerases - chemistry; Carbon-Carbon Double Bond Isomerases - genetics; Carbon-Carbon Double Bond Isomerases - metabolism; Crystallography, X-Ray; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - metabolism; Enzyme Inhibitors - pharmacology; Epoxy Compounds - chemistry; Epoxy Compounds - metabolism; Epoxy Compounds - pharmacology; Escherichia coli - enzymology; Escherichia coli - genetics; Isomerism; Organophosphorus Compounds - chemistry; Organophosphorus Compounds - metabolism; Organophosphorus Compounds - pharmacology; Point Mutation - genetics; Protons
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.10573

Isopentenyl diphosphate:dimethylallyl diphosphate (IPP:DMAPP) isomerase is a key enzyme in the biosynthesis of isoprenoids. The mechanism of the isomerization reaction involves protonation of the unactivated carbon‐carbon double bond in the substrate. Analysis of the 1.97 Å crystal structure of the inactive C67A mutant of E. coli isopentenyl diphosphate:dimethylallyl diphosphate isomerase complexed with the mechanism‐based inactivator 3,4‐epoxy‐3‐methyl‐1‐butyl diphosphate is in agreement with an isomerization mechanism involving Glu 116, Tyr 104, and Cys 67. In particular, the results are consistent with a mechanism where Glu116 is involved in the protonation step and Cys67 in the elimination step. Proteins 2003;53:000–000. © 2003 Wiley‐Liss, Inc.