Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with IPM and MN

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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This is version 1.3 of the entry. See complete history


Atomic Level Description of the Domain Closure in a Dimeric Enzyme: Thermus Thermophilus 3-Isopropylmalate Dehydrogenase.

Graczer, E.Merli, A.Singh, R.K.Karuppasamy, M.Zavodszky, P.Weiss, M.S.Vas, M.

(2011) Mol Biosyst 7: 1646

  • DOI: https://doi.org/10.1039/c0mb00346h
  • Primary Citation of Related Structures:  
    2Y3Z, 2Y40, 2Y41, 2Y42

  • PubMed Abstract: 

    The domain closure associated with the catalytic cycle is described at an atomic level, based on pairwise comparison of the X-ray structures of homodimeric Thermus thermophilus isopropylmalate dehydrogenase (IPMDH), and on their detailed molecular graphical analysis. The structures of the apo-form without substrate and in complex with the divalent metal-ion to 1.8 Å resolution, in complexes with both Mn(2+) and 3-isopropylmalate (IPM), as well as with both Mn(2+) and NADH, were determined at resolutions ranging from 2.0 to 2.5 Å. Single crystal microspectrophotometric measurements demonstrated the presence of a functionally competent protein conformation in the crystal grown in the presence of Mn(2+) and IPM. Structural comparison of the various complexes clearly revealed the relative movement of the two domains within each subunit and allowed the identification of two hinges at the interdomain region: hinge 1 between αd and βF as well as hinge 2 between αh and βE. A detailed analysis of the atomic contacts of the conserved amino acid side-chains suggests a possible operational mechanism of these molecular hinges upon the action of the substrates. The interactions of the protein with Mn(2+) and IPM are mainly responsible for the domain closure: upon binding into the cleft of the interdomain region, the substrate IPM induces a relative movement of the secondary structural elements βE, βF, βG, αd and αh. A further special feature of the conformational change is the movement of the loop bearing the amino acid Tyr139 that precedes the interacting arm of the subunit. The tyrosyl ring rotates and moves by at least 5 Å upon IPM-binding. Thereby, new hydrophobic interactions are formed above the buried isopropyl-group of IPM. Domain closure is then completed only through subunit interactions: a loop of one subunit that is inserted into the interdomain cavity of the other subunit extends the area with the hydrophobic interactions, providing an example of the cooperativity between interdomain and intersubunit interactions.

  • Organizational Affiliation

    Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, PO Box 7, H1518 Budapest, Hungary.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
359Thermus thermophilusMutation(s): 0 
Find proteins for Q5SIY4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SIY4 
Go to UniProtKB:  Q5SIY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SIY4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.24α = 90
b = 146.33β = 90
c = 175.21γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2012-04-18
    Changes: Database references
  • Version 1.2: 2019-07-17
    Changes: Data collection
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description