1Q54

STRUCTURE AND MECHANISM OF ACTION OF ISOPENTENYLPYROPHOSPHATE-DIMETHYLALLYLPYROPHOSPHATE ISOMERASE: COMPLEX WITH THE BROMOHYDRINE OF IPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase.

Wouters, J.Oudjama, Y.Ghosh, S.Stalon, V.Droogmans, L.Oldfield, E.

(2003) J Am Chem Soc 125: 3198-3199

  • DOI: https://doi.org/10.1021/ja029171p
  • Primary Citation of Related Structures:  
    1Q54

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    Institut de Recherche Wiame and Laboratoire de Microbiologie, Universite Libre de Bruxelles, 1 Avenue E. Gryson, 1070 Brussels, Belgium.


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: 1.93 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.83α = 90
b = 71.35β = 90
c = 91.49γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SHELXmodel building
SHELXL-97refinement
SHELXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-26
    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: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-16
    Changes: Data collection, Refinement description