1R67

Y104A MUTANT OF E.COLI IPP ISOMERASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural role for Tyr-104 in Escherichia coli isopentenyl-diphosphate isomerase: site-directed mutagenesis, enzymology, and protein crystallography.

de Ruyck, J.Durisotti, V.Oudjama, Y.Wouters, J.

(2006) J.Biol.Chem. 281: 17864-17869

  • DOI: 10.1074/jbc.M601851200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Isopentenyl-diphosphate (IPP):dimethylallyl diphosphate 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, but ...

    Isopentenyl-diphosphate (IPP):dimethylallyl diphosphate 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, but identity of the acidic moiety providing the proton is still not clear. Multiple sequence alignments and geometrical features observed in crystal structures of complexes with IPP isomerase suggest that Tyr-104 could play an important role during catalysis. A series of mutants was constructed by directed mutagenesis and characterized by enzymology. Crystallographic and thermal denaturation data for Y104A and Y104F mutants were obtained. Those data demonstrate the importance of residue Tyr-104 for proper folding of Escherichia coli type I IPP isomerase.


    Organizational Affiliation

    Laboratoire de Chimie Biologique Structurale, University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium. jerome.deruyck@fundp.ac.be




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isopentenyl-diphosphate delta-isomerase
A
190Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: idi (ygfV)
EC: 5.3.3.2
Find proteins for Q46822 (Escherichia coli (strain K12))
Go to UniProtKB:  Q46822
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.190 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.648α = 90.00
b = 71.648β = 90.00
c = 61.327γ = 120.00
Software Package:
Software NamePurpose
SHELXL-97refinement
SHELXmodel building
SCALEPACKdata scaling
DENZOdata reduction
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2003-10-15 
  • Released Date: 2003-10-21 
  • Deposition Author(s): Wouters, J.

Revision History 

  • Version 1.0: 2003-10-21
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance