Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.98 kDa 
• Atom Count: 3153 
• Modelled Residue Count: 356 
• Deposited Residue Count: 366 
• Unique protein chains: 1

1NFZ

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

• PDB DOI: 10.2210/pdb1NFZ/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-12-16 Released: 2003-06-24 
• Deposition Author(s): Wouters, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.237 
• R-Value Work: 0.176 
• R-Value Observed: 0.181 

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

• PubMed: 12540835 
• DOI: 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. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE	A, B	183	Escherichia coli	Mutation(s): 0  EC: 5.3.3.2
UniProt
Find proteins for Q46822 (Escherichia coli (strain K12)) Explore Q46822  Go to UniProtKB:  Q46822

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EIP	E [auth A], H [auth B]	4-HYDROXY-3-METHYL BUTYL DIPHOSPHATE C5 H14 O8 P2 URURINNTPGGDIV-YFKPBYRVSA-N
MN	C [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.237 
• R-Value Work: 0.176 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.1	α = 90
b = 72.11	β = 90
c = 91.52	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SHELX	model building
SHELXL-97	refinement
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-12-16 
• Released Date: 2003-06-24 
Deposition Author(s): Wouters, J.

Revision History  

• 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: 2018-01-31
  Changes: Experimental preparation
• Version 1.5: 2018-04-04
  Changes: Data collection