1A05

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

• PDB DOI:  https://doi.org/10.2210/pdb1A05/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acidithiobacillus ferrooxidans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-12-09 Released: 1998-06-17 
• Deposition Author(s): Imada, K., Inagaki, K., Matsunami, H., Kawaguchi, H., Tanaka, H., Tanaka, N., Namba, K.

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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 

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: 9739088 
• DOI: https://doi.org/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 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.

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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

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Organizational Affiliation: 

International Institute for Advanced Research, Matsushita Electric Industrial Co., Ltd., Seika, Japan. [e-mail]

Biological Assembly 1  

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: 77.41 kDa 
• Atom Count: 5,914 
• Modelled Residue Count: 714 
• Deposited Residue Count: 716 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-ISOPROPYLMALATE DEHYDROGENASE	A, B	358	Acidithiobacillus ferrooxidans	Mutation(s): 0  Gene Names: leuB EC: 1.1.1.85
UniProt
Find proteins for Q56268 (Acidithiobacillus ferrooxidans) Explore Q56268  Go to UniProtKB:  Q56268

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPM	E [auth A], F [auth B]	3-ISOPROPYLMALIC ACID C7 H12 O5 RNQHMTFBUSSBJQ-CRCLSJGQSA-N
MG	C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 56.54	α = 90
b = 114.24	β = 90
c = 130.89	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
PROCESS	data reduction
PROCESS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-06-17 
Deposition Author(s): Imada, K., Inagaki, K., Matsunami, H., Kawaguchi, H., Tanaka, H., Tanaka, N., Namba, K.

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
• Version 1.3: 2023-08-02
  Changes: Database references, Derived calculations, Other, Refinement description