1A05

CRYSTAL STRUCTURE OF THE COMPLEX OF 3-ISOPROPYLMALATE DEHYDROGENASE FROM THIOBACILLUS FERROOXIDANS WITH 3-ISOPROPYLMALATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: the role of Glu88 in the unique substrate-recognition mechanism.

Imada, K.Inagaki, K.Matsunami, H.Kawaguchi, H.Tanaka, H.Tanaka, N.Namba, K.

(1998) Structure 6: 971-982

  • DOI: 10.1016/s0969-2126(98)00099-9
  • Primary Citation of Related Structures:  
    1A05

  • PubMed Abstract: 
  • 3-Isopropylmalate dehydrogenase (IPMDH) and isocitrate dehydrogenase (ICDH) belong to a unique family of bifunctional decarboxylating dehydrogenases. Although the ICDH dimer catalyzes its reaction under a closed conformation, known structures of the ...

    3-Isopropylmalate dehydrogenase (IPMDH) and isocitrate dehydrogenase (ICDH) belong to a unique family of bifunctional decarboxylating dehydrogenases. Although the ICDH dimer catalyzes its reaction under a closed conformation, known structures of the IPMDH dimer (without substrate) adopt a fully open or a partially closed form. Considering the similarity in the catalytic mechanism, the IPMDH dimer must be in a fully closed conformation during the reaction. A large conformational change should therefore occur upon substrate binding.


    Related Citations: 
    • Overproduction and Substrate Specificity of 3-Isopropylmalate Dehydrogenase from Thiobacillus Ferrooxidans
      Matsunami, H., Kawaguchi, H., Inagaki, K., Eguchi, T., Kakinuma, K., Tanaka, H.
      (1998) Biosci Biotechnol Biochem 62: 372
    • 3-Isopropylmalate Dehydrogenase from Chemolithoautotroph Thiobacillus Ferrooxidans: DNA Sequence, Enzyme Purification, and Characterization
      Kawaguchi, H., Inagaki, K., Kuwata, Y., Tanaka, H., Tano, T.
      (1993) J Biochem 114: 370
    • Cloning and Expression of the Thiobacillus Ferrooxidans 3-Isopropylmalate Dehydrogenase Gene in Escherichia Coli
      Inagaki, K., Kawaguchi, H., Kuwata, Y., Sugio, T., Tanaka, H., Tano, T.
      (1990) J Ferment Bioeng 70: 71

    Organizational Affiliation

    International Institute for Advanced Research, Matsushita Electric Industrial Co., Ltd., Seika, Japan. kimada@npn.jst.go.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-ISOPROPYLMALATE DEHYDROGENASEAB358Acidithiobacillus ferrooxidansMutation(s): 0 
Gene Names: leuB
EC: 1.1.1.85
Find proteins for Q56268 (Acidithiobacillus ferrooxidans)
Explore Q56268 
Go to UniProtKB:  Q56268
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IPM
Query on IPM

Download CCD File 
A, B
3-ISOPROPYLMALIC ACID
C7 H12 O5
RNQHMTFBUSSBJQ-CRCLSJGQSA-N
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.54α = 90
b = 114.24β = 90
c = 130.89γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
PROCESSdata reduction
PROCESSdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-17
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance