Catalytic mechanism of Escherichia coli isopentenyl diphosphate isomerase involves Cys-67, Glu-116, and Tyr-104 as suggested by crystal structures of complexes with transition state analogues and irreversible inhibitors.
Isopentenyl diphosphate (IPP):dimethylallyl diphosphate (DMAPP) isomerase is a key enzyme in the biosynthesis of isoprenoids. The reaction involves protonation and deprotonation of the isoprenoid unit and proceeds through a carbocationic transition state. Analysis of the crystal structures (2 A) of complexes of Escherichia coli IPP.DMAPPs isomerase with a transition state analogue (N,N-dimethyl-2-amino-1-ethyl diphosphate) and a covalently attached irreversible inhibitor (3,4-epoxy-3-methyl-1-butyl diphosphate) indicates that Glu-116, Tyr-104, and Cys-67 are involved in the antarafacial addition/elimination of protons during isomerization. This work provides a new perspective about the mechanism of the reaction.
Wouters
J
J
Institut de Recherches Microbiologiques J.M. Wiame, 1 av E. Gryzon 1070 Bruxelles, Belgium. jwouters@dbm.ulb.ac.be
Oudjama
Y
Y
Barkley
Sam J
SJ
Tricot
C
C
Stalon
V
V
Droogmans
L
L
Poulter
C Dale
CD
D019748:Carbon-Carbon Double Bond Isomerases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism*; D020134:Catalytic Domain; D003461:Crystallography; D003545:Cysteine / Q000737:chemistry; D004852:Epoxy Compounds / Q000494:pharmacology; D004926:Escherichia coli / Q000201:enzymology*; D018698:Glutamic Acid / Q000737:chemistry; D045782:Hemiterpenes; D007700:Kinetics; D009943:Organophosphorus Compounds / Q000494:pharmacology; D017433:Protein Structure, Secondary; D014443:Tyrosine / Q000737:chemistry
D004852:Epoxy Compounds; D045782:Hemiterpenes; D009943:Organophosphorus Compounds; C077385:3-methyl-3,4-epoxybutyl diphosphate; D018698:Glutamic Acid; D014443:Tyrosine; D019748:Carbon-Carbon Double Bond Isomerases; C021453:isopentenyldiphosphate delta-isomerase; D003545:Cysteine