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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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

  • Primary Citation of Related Structures:  

  • 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 subu ...

    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.


    Related Citations: 
    • Differences in the Oligomeric States of the Ldh- Like L-Maldh from the Hyperthermophilic Archaea Methanococcus Jannaschii and Archaeoglobus Fulgidus.
      Madern, D.,Ebel, C.,Dale, H.A.,Lien, T.,Steen, I.H.,Birkeland, N.K.,Zaccai, G.
      (2001) Biochemistry 40: 10310
    • Properties and Primary Structure of a Thermostable L-Malate Dehydrogenase from Archaeoglobus Fulgidus
      Langelandsvik, A.S.,Steen, I.H.,Birkeland, N.K.,Lien, T.
      (1997) Arch.Microbiol. 168: 59


    Organizational Affiliation

    Laboratoire de Biophysique Mol├ęculaire, 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MALATE DEHYDROGENASE
A
294Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)Mutation(s): 0 
Gene Names: mdh
EC: 1.1.1.37
Find proteins for O08349 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Go to UniProtKB:  O08349
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAI
Query on NAI

Download SDF File 
Download CCD File 
A
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.152 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 112.964α = 90.00
b = 112.964β = 90.00
c = 71.294γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
BIOMOLdata scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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