1IPD

THREE-DIMENSIONAL STRUCTURE OF A HIGHLY THERMOSTABLE ENZYME, 3-ISOPROPYLMALATE DEHYDROGENASE OF THERMUS THERMOPHILUS AT 2.2 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Three-dimensional structure of a highly thermostable enzyme, 3-isopropylmalate dehydrogenase of Thermus thermophilus at 2.2 A resolution.

Imada, K.Sato, M.Tanaka, N.Katsube, Y.Matsuura, Y.Oshima, T.

(1991) J Mol Biol 222: 725-738

  • DOI: 10.1016/0022-2836(91)90508-4
  • Primary Citation of Related Structures:  
    1IPD

  • PubMed Abstract: 
  • The three-dimensional structure of the highly thermostable 3-isopropylmalate dehydrogenase (IPMDH) from Thermus thermophilus has been determined by the multiple isomorphous replacement method and refined to 2.2 A resolution. The final R-factor is 0.1 ...

    The three-dimensional structure of the highly thermostable 3-isopropylmalate dehydrogenase (IPMDH) from Thermus thermophilus has been determined by the multiple isomorphous replacement method and refined to 2.2 A resolution. The final R-factor is 0.185 for 20,307 reflections. The crystal asymmetric unit has one subunit consisting of 345 amino acid residues. The polypeptide chain of this subunit is folded into two domains (first and second domains) with parallel alpha/beta motifs. The domains are similar in their conformations and folding topologies, but differ from those of the NAD-binding domains of such well-known enzymes as the alcohol and lactate dehydrogenases. A beta-strand that is a part of the long arm-like polypeptide protruding from the second domain comes into contact with another subunit and contributes to the formation of an isologous dimer with a crystallographic 2-fold symmetry. Close subunit contacts are also present at two alpha-helices in the second domain. These helices strongly interact hydrophobically with the corresponding helices of the other subunit to form a hydrophobic core at the center of the dimer. Two large pockets that exist between the first domain of one subunit and the second domain of the other include the amino acid residues responsible for substrate binding. These results indicate that the dimeric form is essential for the IPMDH to express enzymatic activity and that the close subunit contact at the hydrophobic core is important for the thermal stability of the enzyme.


    Related Citations: 
    • Purification, Catalytic Properties and Thermal Stability of Threo-Ds-3-Isopropylmalate Dehydrogenase Coded by Leub Gene from an Extreme Thermophile, Thermus Thermophilus Strain Hb8
      Yamada, T., Akutsu, N., Miyazaki, K., Kakinuma, K., Yoshida, M., Oshima, T.
      (1990) J Biochem 108: 449
    • Crystallization and Preliminary X-Ray Data for 3-Isopropylmalate Dehydrogenase of Thermus Thermophilus
      Katsube, Y., Tanaka, N., Takenaka, A., Yamada, T., Oshima, T.
      (1988) J Biochem 104: 679

    Organizational Affiliation

    Institute for Protein Research Osaka University, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-ISOPROPYLMALATE DEHYDROGENASEA345Thermus thermophilusMutation(s): 0 
EC: 1.1.1.85
Find proteins for Q5SIY4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SIY4 
Go to UniProtKB:  Q5SIY4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.185 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.6α = 90
b = 78.6β = 90
c = 158.1γ = 120
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other