1OW2 | pdb_00001ow2

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

• PDB DOI: https://doi.org/10.2210/pdb1OW2/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-03-28 Released: 2004-01-20 
• Deposition Author(s): Wouters, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.294 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.228 (Depositor) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

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

• PubMed: 14696183 
• DOI: https://doi.org/10.1002/prot.10573
• Primary Citation 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. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 41.91 kDa 
• Atom Count: 3,022 
• Modeled Residue Count: 356 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE	A, B	183	Escherichia coli	Mutation(s): 1  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: 2.00 Å
• R-Value Free:  0.294 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.228 (Depositor) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.948	α = 90
b = 71.394	β = 90
c = 92.381	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-01-20 
Deposition Author(s): Wouters, J.

Revision History  

• 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