2cmd
From Proteopedia
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| - | [[Image:2cmd.gif|left|200px]] | + | [[Image:2cmd.gif|left|200px]] |
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| - | '''THE CRYSTAL STRUCTURE OF E.COLI MALATE DEHYDROGENASE: A COMPLEX OF THE APOENZYME AND CITRATE AT 1.87 ANGSTROMS RESOLUTION''' | + | {{Structure |
| + | |PDB= 2cmd |SIZE=350|CAPTION= <scene name='initialview01'>2cmd</scene>, resolution 1.87Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=CIT:CITRIC ACID'>CIT</scene> | ||
| + | |ACTIVITY= [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] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''THE CRYSTAL STRUCTURE OF E.COLI MALATE DEHYDROGENASE: A COMPLEX OF THE APOENZYME AND CITRATE AT 1.87 ANGSTROMS RESOLUTION''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2CMD is a [ | + | 2CMD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CMD OCA]. |
==Reference== | ==Reference== | ||
| - | Crystal structure of Escherichia coli malate dehydrogenase. A complex of the apoenzyme and citrate at 1.87 A resolution., Hall MD, Levitt DG, Banaszak LJ, J Mol Biol. 1992 Aug 5;226(3):867-82. PMID:[http:// | + | Crystal structure of Escherichia coli malate dehydrogenase. A complex of the apoenzyme and citrate at 1.87 A resolution., Hall MD, Levitt DG, Banaszak LJ, J Mol Biol. 1992 Aug 5;226(3):867-82. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1507230 1507230] |
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Malate dehydrogenase]] | [[Category: Malate dehydrogenase]] | ||
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[[Category: oxidoreductase(nad(a)-choh(d))]] | [[Category: oxidoreductase(nad(a)-choh(d))]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:17:14 2008'' |
Revision as of 14:17, 20 March 2008
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| , resolution 1.87Å | |||||||
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| Ligands: | |||||||
| Activity: | Malate dehydrogenase, with EC number 1.1.1.37 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
THE CRYSTAL STRUCTURE OF E.COLI MALATE DEHYDROGENASE: A COMPLEX OF THE APOENZYME AND CITRATE AT 1.87 ANGSTROMS RESOLUTION
Overview
The crystal structure of malate dehydrogenase from Escherichia coli has been determined with a resulting R-factor of 0.187 for X-ray data from 8.0 to 1.87 A. Molecular replacement, using the partially refined structure of porcine mitochondrial malate dehydrogenase as a probe, provided initial phases. The structure of this prokaryotic enzyme is closely homologous with the mitochondrial enzyme but somewhat less similar to cytosolic malate dehydrogenase from eukaryotes. However, all three enzymes are dimeric and form the subunit-subunit interface through similar surface regions. A citrate ion, found in the active site, helps define the residues involved in substrate binding and catalysis. Two arginine residues, R81 and R153, interacting with the citrate are believed to confer substrate specificity. The hydroxyl of the citrate is hydrogen-bonded to a histidine, H177, and similar interactions could be assigned to a bound malate or oxaloacetate. Histidine 177 is also hydrogen-bonded to an aspartate, D150, to form a classic His.Asp pair. Studies of the active site cavity indicate that the bound citrate would occupy part of the site needed for the coenzyme. In a model building study, the cofactor, NAD, was placed into the coenzyme site which exists when the citrate was converted to malate and crystallographic water molecules removed. This hypothetical model of a ternary complex was energy minimized for comparison with the structure of the binary complex of porcine cytosolic malate dehydrogenase. Many residues involved in cofactor binding in the minimized E. coli malate dehydrogenase structure are homologous to coenzyme binding residues in cytosolic malate dehydrogenase. In the energy minimized structure of the ternary complex, the C-4 atom of NAD is in van der Waals' contact with the C-3 atom of the malate. A catalytic cycle involves hydride transfer between these two atoms.
About this Structure
2CMD is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Crystal structure of Escherichia coli malate dehydrogenase. A complex of the apoenzyme and citrate at 1.87 A resolution., Hall MD, Levitt DG, Banaszak LJ, J Mol Biol. 1992 Aug 5;226(3):867-82. PMID:1507230
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