1NFS

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 


Literature

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.

(2003) J Biol Chem 278: 11903-11908

  • DOI: https://doi.org/10.1074/jbc.M212823200
  • Primary Citation of Related Structures:  
    1NFS, 1NFZ

  • PubMed Abstract: 

    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.

    • Organizational Affiliation: 

    Institut de Recherches Microbiologiques J.M. Wiame, 1 av E. Gryzon 1070 Bruxelles, Belgium. jwouters@dbm.ulb.ac.be


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE
A, B
183Escherichia coliMutation(s): 0 
EC: 5.3.3.2
UniProt
Find proteins for Q46822 (Escherichia coli (strain K12))
Explore Q46822 
Go to UniProtKB:  Q46822
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46822
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.982α = 90
b = 71.493β = 90
c = 91.441γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SHELXmodel building
SHELXL-97refinement
SHELXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

  • Released Date: 2003-06-24 
    • Deposition Author(s): Wouters, J.

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2018-04-04
    Changes: Data collection
  • Version 1.5: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description