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 Å
  • R-Value Free: 0.275 
  • R-Value Work: 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


  • 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.(Tokyo) 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-ISOPROPYLMALATE DEHYDROGENASE
A, B
358Acidithiobacillus ferrooxidansGene Names: leuB
EC: 1.1.1.85
Find proteins for Q56268 (Acidithiobacillus ferrooxidans)
Go to UniProtKB:  Q56268
Small Molecules
Ligands 2 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
IPM
Query on IPM

Download SDF File 
Download CCD File 
A, B
3-ISOPROPYLMALIC ACID
C7 H12 O5
RNQHMTFBUSSBJQ-CRCLSJGQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 56.540α = 90.00
b = 114.240β = 90.00
c = 130.890γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
PROCESSdata scaling
PROCESSdata reduction
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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