Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase.
We have obtained the three-dimensional X-ray crystallographic structure of a C67A mutant Escherichia coli isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase (EC 5.3.3.2) complexed with the bromohydrin of isopentenylpyrophosphate, at 1.93 A resolution. The overall backbone fold is very similar to that obtained previously for the wild-type enzyme in the presence of a divalent metal cation (Mn2+ or Mg2+). However, in the new structure, there are two metal binding sites, not just one. The first metal binding site is occupied by Mn2+, coordinated to three histidine and two glutamate residues, while the second is occupied by Mg2+, coordinated to two bromohydrin-ligand phosphate oxygens, the carbonyl oxygen of A67, a carboxyl oxygen of E87, and two water molecules. The C3 hydroxyl group of the bromohydrin inhibitor is involved in a short hydrogen bond to the carboxyl group of E116, one of the two Mn-bound glutamates. The structure obtained is consistent with a mechanism of action of the enzyme in which the carboxyl group of E116 protonates the double bond in isopentenylpyrophosphate, forming a carbocation, followed by removal of a C2 proton by the thiolate of C67, in the wild-type enzyme. The inhibition of the enzyme by a wide variety of other potent inhibitors is also readily explained on the basis of the bromohydrin inhibitor structure.
Wouters
Johan
J
Institut de Recherche Wiame and Laboratoire de Microbiologie, Universite Libre de Bruxelles, 1 Avenue E. Gryson, 1070 Brussels, Belgium.
Oudjama
Yamina
Y
Ghosh
Subhash
S
Stalon
Victor
V
Droogmans
Louis
L
Oldfield
Eric
E
D019748:Carbon-Carbon Double Bond Isomerases / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000378:metabolism; D011756:Diphosphates / Q000737:chemistry* / Q000494:pharmacology*; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000494:pharmacology*; D045782:Hemiterpenes; D007700:Kinetics; D008958:Models, Molecular; D011487:Protein Conformation; D013329:Structure-Activity Relationship
D011756:Diphosphates; D004791:Enzyme Inhibitors; D045782:Hemiterpenes; C429553:bromohydrin pyrophosphate; D019748:Carbon-Carbon Double Bond Isomerases; C021453:isopentenyldiphosphate delta-isomerase