5MDH

CRYSTAL STRUCTURE OF TERNARY COMPLEX OF PORCINE CYTOPLASMIC MALATE DEHYDROGENASE ALPHA-KETOMALONATE AND TNAD AT 2.4 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD.

Chapman, A.D.Cortes, A.Dafforn, T.R.Clarke, A.R.Brady, R.L.

(1999) J Mol Biol 285: 703-712

  • DOI: 10.1006/jmbi.1998.2357
  • Primary Citation of Related Structures:  
    5MDH

  • PubMed Abstract: 
  • The structural basis for the extreme discrimination achieved by malate dehydrogenases between a variety of closely related substrates encountered within the cell has been difficult to assess because of the lack of an appropriate catalytically competent structure of the enzyme ...

    The structural basis for the extreme discrimination achieved by malate dehydrogenases between a variety of closely related substrates encountered within the cell has been difficult to assess because of the lack of an appropriate catalytically competent structure of the enzyme. Here, we have determined the crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase with the alternative substrate alpha-ketomalonate and the coenzyme analogue 1,4,5,6-tetrahydronicotinamide. Both subunits of the dimeric porcine heart, and from the prokaryotes Escherichia coli and Thermus flavus. However, large changes are noted around the active site, where a mobile loop now closes to bring key residues into contact with the substrate. This observation substantiates a postulated mechanism in which the enzyme achieves high levels of substrate discrimination through charge balancing in the active site. As the activated cofactor/substrate complex has a net negative charge, a positive counter-charge is provided by a conserved arginine in the active site loop. The enzyme must, however, also discriminate against smaller substrates, such as pyruvate. The structure shows in the closed (loop down) catalytically competent complex two arginine residues (91 and 97) are driven into close proximity. Without the complimentary, negative charge of the substrate side-chain of oxaloacetate or alpha-ketomalonate, charge repulsion would resist formation production of this catalytically productive conformation, hence minimising the effectiveness of pyruvate as a substrate. By this mechanism, malate dehydrogenase uses charge balancing to achieve fivefold orders of magnitude in discrimination between potential substrates.


    Related Citations: 
    • Refined Crystal Structure of Cytoplasmic Malate Dehydrogenase at 2.5-A Resolution
      Birktoft, J.J., Rhodes, G., Banaszak, L.J.
      (1989) Biochemistry 28: 6065
    • 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
    • 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 U S A 79: 6166
    • 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
    • Conformation of Nicotinamide Adenine Dinucleotide Bound to Cytoplasmic Malate Dehydrogenase
      Webb, L.E., Hill, E.J., Banaszak, L.J.
      (1973) Biochemistry 12: 5101
    • 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
    • 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
    • Cytoplasmic Malate Dehydrogenase--Heavy Atom Derivatives and Low Resolution Structure
      Tsernoglou, D., Hill, E., Banaszak, L.J.
      (1972) J Mol Biol 69: 75
    • Structural Studies on Heart Muscle Malate Dehydrogenases
      Tsernoglou, D., Hill, E., Banaszak, L.J.
      (1972) Cold Spring Harb Symp Quant Biol 36: 171

    Organizational Affiliation

    Department of Biochemistry, University of Briston, BS8 1TD, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MALATE DEHYDROGENASEA, B333Sus scrofaMutation(s): 0 
Gene Names: MDH1
EC: 1.1.1.37
UniProt
Find proteins for P11708 (Sus scrofa)
Explore P11708 
Go to UniProtKB:  P11708
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
MAK
Query on MAK

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]ALPHA-KETOMALONIC ACID
C3 H2 O5
XEEVLJKYYUVTRC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.7α = 90
b = 144.432β = 90
c = 59.226γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-18
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-08-17
    Changes: Derived calculations