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 
  • R-Value Observed: 0.211 

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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

  • DOI: 10.1021/bi00174a014
  • Primary Citation of Related Structures:  
    1MLD

  • 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 point symmetry in the crystal ...

    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: 
    • 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
    • Refined Crystal Structure of Cytoplasmic Malate Dehydrogenase at 2.5 Angstroms Resolution
      Birktoft, J.J., Rhodes, G., Banaszak, L.J.
      (1989) Biochemistry 28: 6065
    • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MALATE DEHYDROGENASEA, B, C, D314Sus scrofaMutation(s): 0 
Gene Names: MDH2
EC: 1.1.1.37
UniProt
Find proteins for P00346 (Sus scrofa)
Explore P00346 
Go to UniProtKB:  P00346
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00346
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.75α = 90
b = 146.76β = 108.16
c = 67.58γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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