5mdh
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CRYSTAL STRUCTURE OF TERNARY COMPLEX OF PORCINE CYTOPLASMIC MALATE DEHYDROGENASE ALPHA-KETOMALONATE AND TNAD AT 2.4 ANGSTROMS RESOLUTION
OverviewOverview
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.
About this StructureAbout this Structure
5MDH is a Single protein structure of sequence from Sus scrofa with NAD and MAK as ligands. Active as Malate dehydrogenase, with EC number 1.1.1.37 Full crystallographic information is available from OCA.
ReferenceReference
Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD., Chapman AD, Cortes A, Dafforn TR, Clarke AR, Brady RL, J Mol Biol. 1999 Jan 15;285(2):703-12. PMID:10075524
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