1HZT

CRYSTAL STRUCTURE OF METAL-FREE ISOPENTENYL DIPHOSPHATE:DIMETHYLALLYL DIPHOSPHATE ISOMERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of isopentenyl diphosphate:dimethylallyl diphosphate isomerase.

Durbecq, V.Sainz, G.Oudjama, Y.Clantin, B.Bompard-Gilles, C.Tricot, C.Caillet, J.Stalon, V.Droogmans, L.Villeret, V.

(2001) EMBO J 20: 1530-1537

  • DOI: 10.1093/emboj/20.7.1530
  • Primary Citation of Related Structures:  
    1HX3, 1HZT

  • PubMed Abstract: 
  • Isopentenyl diphosphate:dimethylallyl diphosphate (IPP:DMAPP) isomerase catalyses a crucial activation step in the isoprenoid biosynthesis pathway. This enzyme is responsible for the isomerization of the carbon-carbon double bond of IPP to create the ...

    Isopentenyl diphosphate:dimethylallyl diphosphate (IPP:DMAPP) isomerase catalyses a crucial activation step in the isoprenoid biosynthesis pathway. This enzyme is responsible for the isomerization of the carbon-carbon double bond of IPP to create the potent electrophile DMAPP. DMAPP then alkylates other molecules, including IPP, to initiate the extraordinary variety of isoprenoid compounds found in nature. The crystal structures of free and metal-bound Escherichia coli IPP isomerase reveal critical active site features underlying its catalytic mechanism. The enzyme requires one Mn(2+) or Mg(2+) ion to fold in its active conformation, forming a distorted octahedral metal coordination site composed of three histidines and two glutamates and located in the active site. Two critical residues, C67 and E116, face each other within the active site, close to the metal-binding site. The structures are compatible with a mechanism in which the cysteine initiates the reaction by protonating the carbon-carbon double bond, with the antarafacial rearrangement ultimately achieved by one of the glutamates involved in the metal coordination sphere. W161 may stabilize the highly reactive carbocation generated during the reaction through quadrupole- charge interaction.


    Organizational Affiliation

    Laboratoire de Microbiologie, Université Libre de Bruxelles, 1 avenue E.Gryson, 1070 Bruxelles, Belgium.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ISOPENTENYL DIPHOSPHATE DELTA-ISOMERASEA190Escherichia coliMutation(s): 0 
Gene Names: idi
EC: 5.3.3.2
Find proteins for Q46822 (Escherichia coli (strain K12))
Explore Q46822 
Go to UniProtKB:  Q46822
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.4α = 90
b = 71.4β = 90
c = 61.85γ = 120
Software Package:
Software NamePurpose
SOLVEphasing
MLPHAREphasing
WARPmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
ARP/wARPmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-07-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance