5MDH

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

Summary for 5MDH

• Entry DOI: 10.2210/pdb5mdh/pdb
• Descriptor: MALATE DEHYDROGENASE, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ALPHA-KETOMALONIC ACID, ... (4 entities in total)
• Functional Keywords: oxidoreductase, (nad(a)-choh(d))
• Biological source: Sus scrofa (pig)
• Cellular location: Cytoplasm: P11708
• Total number of polymer chains: 2
• Total formula weight: 74298.82

Authors

Chapman, A.D.M.,Cortes, A.,Dafforn, T.R.,Clarke, A.R.,Brady, R.L. (deposition date: 1998-10-08, release date: 1999-05-18, Last modification date: 2023-08-09)

Primary citation

Chapman, A.D.,Cortes, A.,Dafforn, T.R.,Clarke, A.R.,Brady, R.L.
Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD.
J.Mol.Biol., 285:703-712, 1999

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. 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.

PubMed: 10075524
DOI: 10.1006/jmbi.1998.2357

Experimental method

X-RAY DIFFRACTION (2.4 Å)