Crystal Structure of Ignicoccus islandicus malate dehydrogenase co-crystallized with 10 mM Tb-Xo4

Experimental Data Snapshot

  • Resolution: 1.89 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

    wwPDB Validation   3D Report Full Report

    This is version 1.2 of the entry. See complete history


    The archaeal LDH-like malate dehydrogenase from Ignicoccus islandicus displays dual substrate recognition, hidden allostery and a non-canonical tetrameric oligomeric organization.

    Roche, J.Girard, E.Mas, C.Madern, D.

    (2019) J Struct Biol 208: 7-17

    • DOI: https://doi.org/10.1016/j.jsb.2019.07.006
    • Primary Citation of Related Structures:  

    • PubMed Abstract: 

      The NAD(P)-dependent malate dehydrogenases (MalDHs) and NAD-dependent lactate dehydrogenases (LDHs) are homologous enzymes involved in central metabolism. They display a common protein fold and the same catalytic mechanism, yet have a stringent capacity to discriminate between their respective substrates. The MalDH/LDH superfamily is divided into several phylogenetically related groups. It has been shown that the canonical LDHs and LDH-like group of MalDHs are primarily tetrameric enzymes that diverged from a common ancestor. In order to gain understanding of the evolutionary history of the LDHs and MalDHs, the biochemical properties and crystallographic structure of the LDH-like MalDH from the hyperthermophilic archaeon Ignicoccus islandicus (I. isl) were determined. I. isl MalDH recognizes oxaloacetate as main substrate, but it is also able to use pyruvate. Surprisingly, with pyruvate, the enzymatic activity profile looks like that of allosteric LDHs, suggesting a hidden allosteric capacity in a MalDH. The I. isl MalDH tetrameric structure in the apo state is considerably different from those of canonical LDH-like MalDHs and LDHs, representing an alternative oligomeric organization. A comparison with MalDH and LDH counterparts provides strong evidence that the divergence between allosteric and non-allosteric members of the superfamily involves homologs with intermediate, atypical properties.

    • Organizational Affiliation

      Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France.

    Find similar proteins by:  (by identity cutoff)  |  3D Structure
    Entity ID: 1
    MoleculeChains Sequence LengthOrganismDetailsImage
    Malate dehydrogenase
    A, B, C, D
    310Ignicoccus islandicus DSM 13165Mutation(s): 0 
    Gene Names: EYM_03995
    Find proteins for A0A0U3FQH7 (Ignicoccus islandicus DSM 13165)
    Explore A0A0U3FQH7 
    Go to UniProtKB:  A0A0U3FQH7
    Entity Groups  
    Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
    UniProt GroupA0A0U3FQH7
    Sequence Annotations
    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChains Name / Formula / InChI Key2D Diagram3D Interactions
    Query on 7MT

    Download Ideal Coordinates CCD File 
    E [auth A],
    V [auth D]
    C20 H23 N5 O4 Tb
    Query on TB

    Download Ideal Coordinates CCD File 
    AA [auth D]
    F [auth A]
    G [auth A]
    H [auth A]
    I [auth A]
    AA [auth D],
    F [auth A],
    G [auth A],
    H [auth A],
    I [auth A],
    L [auth B],
    M [auth B],
    N [auth B],
    O [auth B],
    Q [auth C],
    R [auth C],
    S [auth C],
    T [auth C],
    U [auth C],
    W [auth D],
    X [auth D],
    Y [auth D],
    Z [auth D]
    Query on CL

    Download Ideal Coordinates CCD File 
    J [auth A],
    K [auth A],
    P [auth B]
    Experimental Data & Validation

    Experimental Data

    • Resolution: 1.89 Å
    • R-Value Free: 0.233 
    • R-Value Work: 0.205 
    • R-Value Observed: 0.206 
    • Space Group: P 2 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 78.486α = 90
    b = 109.017β = 90
    c = 151.91γ = 90
    Software Package:
    Software NamePurpose
    XDSdata reduction
    SCALAdata scaling

    Structure Validation

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    Entry History & Funding Information

    Deposition Data

    Funding OrganizationLocationGrant Number
    French National Research AgencyFranceANR-16-CE11-0011

    Revision History  (Full details and data files)

    • Version 1.0: 2019-07-17
      Type: Initial release
    • Version 1.1: 2019-07-24
      Changes: Data collection, Database references
    • Version 1.2: 2019-09-25
      Changes: Data collection, Database references