4MDH

REFINED CRYSTAL STRUCTURE OF CYTOPLASMIC MALATE DEHYDROGENASE AT 2.5-ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Refined crystal structure of cytoplasmic malate dehydrogenase at 2.5-A resolution.

Birktoft, J.J.Rhodes, G.Banaszak, L.J.

(1989) Biochemistry 28: 6065-6081

  • Also Cited By: 2CVQ, 1Y7T, 1WZI, 1WZE

  • PubMed Abstract: 
  • The molecular structure of cytoplasmic malate dehydrogenase from pig heart has been refined by alternating rounds of restrained least-squares methods and model readjustment on an interactive graphics system. The resulting structure contains 333 amino ...

    The molecular structure of cytoplasmic malate dehydrogenase from pig heart has been refined by alternating rounds of restrained least-squares methods and model readjustment on an interactive graphics system. The resulting structure contains 333 amino acids in each of the two subunits, 2 NAD molecules, 471 solvent molecules, and 2 large noncovalently bound molecules that are assumed to be sulfate ions. The crystallographic study was done on one entire dimer without symmetry restraints. Analysis of the relative position of the two subunits shows that the dimer does not obey exact 2-fold rotational symmetry; instead, the subunits are related by a 173 degrees rotation. The structure results in a R factor of 16.7% for diffraction data between 6.0 and 2.5 A, and the rms deviations from ideal bond lengths and angles are 0.017 A and 2.57 degrees, respectively. The bound coenzyme in addition to hydrophobic interactions makes numerous hydrogen bonds that either are directly between NAD and the enzyme or are with solvent molecules, some of which in turn are hydrogen bonded to the enzyme. The carboxamide group of NAD is hydrogen bonded to the side chain of Asn-130 and via a water molecule to the backbone nitrogens of Leu-157 and Asp-158 and to the carbonyl oxygen of Leu-154. Asn-130 is one of the corner residues in a beta-turn that contains the lone cis peptide bond in cytoplasmic malate dehydrogenase, situated between Asn-130 and Pro-131. The active site histidine, His-186, is hydrogen bonded from nitrogen ND1 to the carboxylate of Asp-158 and from its nitrogen NE2 to the sulfate ion bound in the putative substrate binding site. In addition to interacting with the active site histidine, this sulfate ion is also hydrogen bonded to the guanidinium group of Arg-161, to the carboxamide group of Asn-140, and to the hydroxyl group of Ser-241. It is speculated that the substrate, malate or oxaloacetate, is bound in the sulfate binding site with the substrate 1-carboxyl hydrogen bonded to the guanidinium group of Arg-161.


    Related Citations: 
    • Nicotinamide Adenine Dinucleotide and the Active Site of Cytoplasmic Malate Dehydrogenase
      Banaszak, L.J.,Webb, L.E.
      (1975) STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN --: 375
    • Polypeptide Conformation of Cytoplasmic Malate Dehydrogenase from an Electron Density Map at 3.0 Angstroms Resolution
      Hill, E.,Tsernoglou, D.,Webb, L.,Banaszak, L.J.
      (1972) J.Mol.Biol. 72: 577
    • Cytoplasmic Malate Dehydrogenase-Heavy Atom Derivatives and Low Resolution Structure
      Tsernoglou, D.,Hill, E.,Banaszak, L.J.
      (1972) J.Mol.Biol. 69: 75
    • Comparison of the Molecular Structures of Cytoplasmic and Mitochondrial Malate Dehydrogenase
      Birktoft, J.J.,Fu, Z.,Carnahan, G.E.,Rhodes, G.,Roderick, S.L.,Banaszak, L.J.
      () TO BE PUBLISHED --: --
    • Structure of Porcine Heart Cytoplasmic Malate Dehydrogenase. Combining X-Ray Diffraction and Chemical Sequence Data in Structural Studies
      Birktoft, J.J.,Bradshaw, R.A.,Banaszak, L.J.
      (1987) Biochemistry 26: 2722
    • Structural Studies on Heart Muscle Malate Dehydrogenases
      Tsernoglou, D.,Hill, E.,Banaszak, L.J.
      (1972) Cold Spring Harbor Symp.Quant.Biol. 36: 171
    • The Identification of an Asymmetric Complex of Nicotinamide Adenine Dinucleotide and Pig Heart Cytoplasmic Malate Dehydrogenase
      Glatthaar, B.E.,Banaszak, L.J.,Bradshaw, R.A.
      (1972) Biochem.Biophys.Res.Commun. 46: 757
    • The Presence of a Histidine-Aspartic Acid Pair in the Active Site of 2-Hydroxyacid Dehydrogenases. X-Ray Refinement of Cytoplasmic Malate Dehydrogenase
      Birktoft, J.J.,Banaszak, L.J.
      (1983) J.Biol.Chem. 258: 472
    • The Interactions of Nad/Nadh with 2-Hydroxy Acid Dehydrogenases
      Birktoft, J.J.,Fernley, R.T.,Bradshaw, R.A.,Banaszak, L.J.
      (1982) Molecular Structure and Biological Activity --: 37
    • Amino Acid Sequence Homology Among the 2-Hydroxy Acid Dehydrogenases. Mitochondrial and Cytoplasmic Malate Dehydrogenases Form a Homologous System with Lactate Dehydrogenase
      Birktoft, J.J.,Fernley, R.T.,Bradshaw, R.A.,Banaszak, L.J.
      (1982) Proc.Natl.Acad.Sci.USA 79: 6166
    • Conformation of Nicotinamide Adenine Dinucleotide Bound to Cytoplasmic Malate Dehydrogenase
      Webb, L.E.,Hill, E.J.,Banaszak, L.J.
      (1973) Biochemistry 12: 5101


    Organizational Affiliation

    Department of Biological Chemistry, Washington University School of Medicine, St. Louis, Missouri 63110.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOPLASMIC MALATE DEHYDROGENASE
A, B
334Sus scrofaMutation(s): 0 
Gene Names: MDH1
EC: 1.1.1.37
Find proteins for P11708 (Sus scrofa)
Go to Gene View: MDH1
Go to UniProtKB:  P11708
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A, B
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 139.200α = 90.00
b = 86.600β = 90.00
c = 58.800γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1989-04-19
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other