2X0I

2.9 A RESOLUTION STRUCTURE OF MALATE DEHYDROGENASE FROM ARCHAEOGLOBUS FULGIDUS IN COMPLEX WITH NADH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The 2.9A Resolution Crystal Structure of Malate Dehydrogenase from Archaeoglobus Fulgidus: Mechanisms of Oligomerisation and Thermal Stabilisation.

Irimia, A.Vellieux, F.M.D.Madern, D.Zaccai, G.Karshikoff, A.Tibbelin, G.Ladenstein, R.Lien, T.Birkeland, N.-K.

(2004) J Mol Biol 335: 343

  • DOI: https://doi.org/10.1016/j.jmb.2003.10.054
  • Primary Citation of Related Structures:  
    2X0I, 2X0J

  • PubMed Abstract: 

    The crystal structure of malate dehydrogenase from the hyperthermophilic archaeon Archeoglobus fulgidus, in complex with its cofactor NAD, was solved at 2.9A resolution. The crystal structure shows a compact homodimer with one coenzyme bound per subunit. The substrate binding site is occupied by a sulphate ion. In order to gain insight into adaptation mechanisms, which allow the protein to be stable and active at high temperatures, the 3D structure was compared to those of several thermostable and hyperthermostable homologues, and to halophilic malate dehydrogenase. The hyperthermostable A. fulgidus MalDH protein displays a reduction of the solvent-exposed surface, an optimised compact hydrophobic core, a high number of hydrogen bonds, and includes a large number of ion pairs at the protein surface. These features occur concomitantly with a reduced number of residues in the protein subunit, due to several deletions in loop regions. The loops are further stiffened by ion pair links with secondary structure elements. A. fulgidus malate dehydrogenase is the only dimeric protein known to date that belongs to the [LDH-like] MalDH family. All the other known members of this family are homo-tetramers. The crystal structures revealed that the association of the dimers to form tetramers is prevented by several deletions, taking place at the level of two loops that are known to be essential for the tetramerisation process within the LDH and [LDH-like] MalDH enzymes.


  • Organizational Affiliation

    Laboratoire de Biophysique Moléculaire, Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF, UMR-5075, 41 rue Jules Horowitz, 38027 Cedex 01, Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MALATE DEHYDROGENASE294Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
EC: 1.1.1.37
UniProt
Find proteins for O08349 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O08349 
Go to UniProtKB:  O08349
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO08349
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.156 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.964α = 90
b = 112.964β = 90
c = 71.294γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
BIOMOLdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description