1MLD

REFINED STRUCTURE OF MITOCHONDRIAL MALATE DEHYDROGENASE FROM PORCINE HEART AND THE CONSENSUS STRUCTURE FOR DICARBOXYLIC ACID OXIDOREDUCTASES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refined crystal structure of mitochondrial malate dehydrogenase from porcine heart and the consensus structure for dicarboxylic acid oxidoreductases.

Gleason, W.B.Fu, Z.Birktoft, J.Banaszak, L.

(1994) Biochemistry 33: 2078-2088


  • PubMed Abstract: 
  • The crystal structure of mitochondrial malate dehydrogenase from porcine heart contains four identical subunits in the asymmetric unit of a monoclinic cell. Although the molecule functions as a dimer in solution, it exists as a tetramer with 222 poin ...

    The crystal structure of mitochondrial malate dehydrogenase from porcine heart contains four identical subunits in the asymmetric unit of a monoclinic cell. Although the molecule functions as a dimer in solution, it exists as a tetramer with 222 point symmetry in the crystal. The crystallographic refinement was facilitated in the early stages by using weak symmetry restraints and molecular dynamics. The R-factor including X-ray data to 1.83-A resolution was 21.1%. The final root mean square deviation from canonical values is 0.015 A for bond lengths and 3.2 degrees for bond angles. The resulting model of the tetramer includes independent coordinates for each of the four subunits allowing an internal check on the accuracy of the model. The crystalline mitochondrial malate dehydrogenase tetramer has been analyzed to determine the surface areas lost at different subunit-subunit interfaces. The results show that the interface with the largest surface area is the same one found in cytosolic malate dehydrogenase. Each of the subunits contains a bound citrate molecule in the active site permitting the elaboration of a model for substrate binding which agrees with that found for the crystalline enzyme from Escherichia coli. The environment of the N-terminal region of the crystallographic model has been studied because the functional protein is produced from a precursor. This precursor form has an additional 24 residues which are involved in mitochondrial targeting and, possibly, translocation. The crystallographic model of mitochondrial malate dehydrogenase has been compared with its cytosolic counterpart from porcine heart and two prokaryotic enzymes. Small but significant differences have been found in the polar versus nonpolar accessible surface areas between the mitochondrial and cytosolic enzymes. Using least squares methods, four different malate dehydrogenases have been superimposed and their consensus structure has been determined. An amino acid sequence alignment based on the crystallographic structures describes all the conserved positions. The consensus active site of these dicarboxylic acid dehydrogenases is derived from the least squares comparison.


    Related Citations: 
    • Refined Crystal Structure of Cytoplasmic Malate Dehydrogenase at 2.5 Angstroms Resolution
      Birktoft, J.J.,Rhodes, G.,Banaszak, L.J.
      (1989) Biochemistry 28: 6065
    • Determinants of Protein Thermostability Observed in the 1.9 Angstrom Crystal Structure of Malate Dehydrogenase from the Thermophilic Bacterium Thermus Flavus
      Kelly, C.A.,Nishiyama, M.,Ohnishi, Y.,Beppu, T.,Birktoft, J.J.
      (1993) Biochemistry 32: 3913
    • Comparison of the Molecular Structures of Cytoplasmic and Mitochondrial Malate Dehydrogenases
      Birktoft, J.J.,Fu, Z.,Carnahan, G.E.,Rodes, G.,Roderick, S.L.,Banaszak, L.J.
      (1989) Biochem.Soc.Trans. 17: 301
    • The Three Dimensional Structure of Porcine Heart Mitochondrial Malate Dehydrogenase at 3.0 Angstrom Resolution
      Roderick, S.L.,Banaszak, L.J.
      (1986) J.Biol.Chem. 261: 9461


    Organizational Affiliation

    Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis 55455.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MALATE DEHYDROGENASE
A, B, C, D
314Sus scrofaMutation(s): 0 
Gene Names: MDH2
EC: 1.1.1.37
Find proteins for P00346 (Sus scrofa)
Go to Gene View: MDH2
Go to UniProtKB:  P00346
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A, B, C, D
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Work: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.750α = 90.00
b = 146.760β = 108.16
c = 67.580γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-01-26
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance