1OW2

STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX OF C67A MUTANT WITH EIPP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history. 


Literature

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

Wouters, J., Oudjama, Y., Stalon, V., Droogmans, L., Poulter, C.D.

(2004) Proteins 54: 216-221

  • DOI: https://doi.org/10.1002/prot.10573
  • Primary Citation of Related Structures:  
    1OW2

  • PubMed Abstract: 

    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 A 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.

    • Organizational Affiliation: 

    Institut de Recherches Microbiologiques J.M. Wiame, Bruxelles, Belgium. [email protected]


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): 1 
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: 2.00 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.948α = 90
b = 71.394β = 90
c = 92.381γ = 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: 2004-01-20 
    • Deposition Author(s): Wouters, J.

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-20
    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: Advisory, Refinement description
  • Version 1.4: 2021-10-27
    Changes: Advisory, Database references, Derived calculations
  • Version 1.5: 2023-08-16
    Changes: Data collection, Refinement description
  • Version 1.6: 2024-11-13
    Changes: Structure summary