ISDA

Entry Detail

PDB ID:

1NFS

Keywords:

ISOMERASE

Title:

STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH NIPP

Biological Source:

Source Organism:

Escherichia coli

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2002-12-16

Release Date:

2003-06-24

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.96 Å

R-Value Free:

0.26

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE
Chain IDs:A, B
Chain Length:183
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:Q46822 Pfam ID:PF00293 EC:5.3.3.2

Ligand Molecules

DED

Primary Citation

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

Wouters, J, Oudjama, Y, Barkley, S.J, Tricot, C, Stalon, V, Droogmans, L, Poulter, C.D.Show

J.Biol.Chem. 278 11903 11908 (2003)

PMID: 12540835 DOI: 10.1074/jbc.M212823200

Abstact

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.

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