2ICK

Human isopentenyl diphophate isomerase complexed with substrate analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The crystal structure of human isopentenyl diphosphate isomerase at 1.7 A resolution reveals its catalytic mechanism in isoprenoid biosynthesis

Zheng, W.Sun, F.Bartlam, M.Li, X.Li, R.Rao, Z.

(2007) J.Mol.Biol. 366: 1447-1458

  • DOI: 10.1016/j.jmb.2006.12.055
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Isopentenyl diphosphate isomerase catalyses a crucial activation step in the biosynthesis of isoprenoids, one of the most ancient and diverse classes of natural products. This enzyme is responsible for an unusual isomerization of the inactive carbon- ...

    Isopentenyl diphosphate isomerase catalyses a crucial activation step in the biosynthesis of isoprenoids, one of the most ancient and diverse classes of natural products. This enzyme is responsible for an unusual isomerization of the inactive carbon-carbon double bond of isopentenyl diphosphate (IPP) to create its electrophilic allylic isomer dimethylallyl diphosphate (DMAPP). Here we report the crystal structure of human IPP isomerase at 1.7 A resolution and the complex structure with its native substrate at 1.9 A resolution. These structures reveal a mechanism wherein interconversion is catalyzed by a stereoselective antarafacial [1.3] transposition of a proton involving the indispensable residues Cys87, Glu149, Trp197 and Tyr137. A newly identified alternative conformation of Cys87 driven by Trp197 and the selectivity of different metal ions located in the active site provide further insight into the catalytic mechanism. Comparison with Escherichia coli IPP isomerase reveals a novel substrate entrance in human IPP isomerase.


    Organizational Affiliation

    Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isopentenyl-diphosphate delta isomerase
A
233Homo sapiensMutation(s): 0 
Gene Names: IDI1
EC: 5.3.3.2
Find proteins for Q13907 (Homo sapiens)
Go to Gene View: IDI1
Go to UniProtKB:  Q13907
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
DMA
Query on DMA

Download SDF File 
Download CCD File 
A
DIMETHYLALLYL DIPHOSPHATE
C5 H12 O7 P2
CBIDRCWHNCKSTO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.812α = 90.00
b = 47.396β = 90.00
c = 116.817γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MAR345dtbdata collection
HKL-2000data scaling
HKL-2000data reduction
CNSphasing
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description