5mdh: Difference between revisions
New page: left|200px<br /><applet load="5mdh" size="450" color="white" frame="true" align="right" spinBox="true" caption="5mdh, resolution 2.4Å" /> '''CRYSTAL STRUCTURE OF ... |
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[[Image:5mdh.gif|left|200px]]<br /><applet load="5mdh" size=" | [[Image:5mdh.gif|left|200px]]<br /><applet load="5mdh" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="5mdh, resolution 2.4Å" /> | caption="5mdh, resolution 2.4Å" /> | ||
'''CRYSTAL STRUCTURE OF TERNARY COMPLEX OF PORCINE CYTOPLASMIC MALATE DEHYDROGENASE ALPHA-KETOMALONATE AND TNAD AT 2.4 ANGSTROMS RESOLUTION'''<br /> | '''CRYSTAL STRUCTURE OF TERNARY COMPLEX OF PORCINE CYTOPLASMIC MALATE DEHYDROGENASE ALPHA-KETOMALONATE AND TNAD AT 2.4 ANGSTROMS RESOLUTION'''<br /> | ||
==Overview== | ==Overview== | ||
The structural basis for the extreme discrimination achieved by malate | 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 Structure== | ==About this Structure== | ||
5MDH is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa] with NAD and MAK as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Malate_dehydrogenase Malate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.37 1.1.1.37] Full crystallographic information is available from [http:// | 5MDH is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa] with <scene name='pdbligand=NAD:'>NAD</scene> and <scene name='pdbligand=MAK:'>MAK</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Malate_dehydrogenase Malate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.37 1.1.1.37] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MDH OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Sus scrofa]] | [[Category: Sus scrofa]] | ||
[[Category: Brady, R | [[Category: Brady, R L.]] | ||
[[Category: Chapman, A | [[Category: Chapman, A D.M.]] | ||
[[Category: Clarke, A | [[Category: Clarke, A R.]] | ||
[[Category: Cortes, A.]] | [[Category: Cortes, A.]] | ||
[[Category: Dafforn, T | [[Category: Dafforn, T R.]] | ||
[[Category: MAK]] | [[Category: MAK]] | ||
[[Category: NAD]] | [[Category: NAD]] | ||
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[[Category: oxidoreductase]] | [[Category: oxidoreductase]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:15:34 2008'' | ||
Revision as of 20:15, 21 February 2008
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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 and 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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