4ajs
From Proteopedia
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| - | [[ | + | ==3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with isocitrate, magnesium(II), Adenosine 2',5'-biphosphate and ribosylnicotinamide-5'-phosphate== |
| + | <StructureSection load='4ajs' size='340' side='right' caption='[[4ajs]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[4ajs]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AJS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AJS FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=A2P:ADENOSINE-2-5-DIPHOSPHATE'>A2P</scene>, <scene name='pdbligand=ICT:ISOCITRIC+ACID'>ICT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NMN:BETA-NICOTINAMIDE+RIBOSE+MONOPHOSPHATE'>NMN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ai2|1ai2]], [[1ai3|1ai3]], [[1bl5|1bl5]], [[1cw1|1cw1]], [[1cw4|1cw4]], [[1cw7|1cw7]], [[1gro|1gro]], [[1grp|1grp]], [[1hj6|1hj6]], [[1idc|1idc]], [[1idd|1idd]], [[1ide|1ide]], [[1idf|1idf]], [[1ika|1ika]], [[1iso|1iso]], [[1p8f|1p8f]], [[1pb1|1pb1]], [[1pb3|1pb3]], [[1sjs|1sjs]], [[3icd|3icd]], [[4ajr|4ajr]], [[4icd|4icd]], [[5icd|5icd]], [[6icd|6icd]], [[7icd|7icd]], [[8icd|8icd]], [[9icd|9icd]]</td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ajs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ajs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ajs RCSB], [http://www.ebi.ac.uk/pdbsum/4ajs PDBsum]</span></td></tr> | ||
| + | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | NADP(+) dependent isocitrate dehydrogenase (IDH; EC 1.1.1.42) belongs to a large family of alpha-hydroxyacid oxidative beta-decarboxylases that catalyze similar three-step reactions, with dehydrogenation to an oxaloacid intermediate preceding beta-decarboxylation to an enol intermediate followed by tautomerization to the final alpha-ketone product. A comprehensive view of the induced fit needed for catalysis is revealed on comparing the first "fully closed" crystal structures of a pseudo-Michaelis complex of wild-type Escherichia coli IDH (EcoIDH) and the "fully closed" reaction product complex of the K100M mutant with previously obtained "quasi-closed" and "open" conformations. Conserved catalytic residues, binding the nicotinamide ring of NADP(+) and the metal-bound substrate, move as rigid bodies during domain closure by a hinge motion that spans the central beta-sheet in each monomer. Interactions established between Thr105 and Ser113, which flank the "phosphorylation loop", and the nicotinamide mononucleotide moiety of NADP(+) establish productive coenzyme binding. Electrostatic interactions of a Lys100-Leu103-Asn115-Glu336 tetrad play a pivotal role in assembling a catalytically competent active site. As predicted, Lys230* is positioned to deprotonate/reprotonate the alpha-hydroxyl in both reaction steps and Tyr160 moves into position to protonate C3 following beta-decarboxylation. A proton relay from the catalytic triad Tyr160-Asp307-Lys230* connects the alpha-hydroxyl of isocitrate to the bulk solvent to complete the picture of the catalytic mechanism. | ||
| - | + | Induced fit and the catalytic mechanism of isocitrate dehydrogenase.,Goncalves S, Miller SP, Carrondo MA, Dean AM, Matias PM Biochemistry. 2012 Sep 11;51(36):7098-115. Epub 2012 Aug 27. PMID:22891681<ref>PMID:22891681</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| - | + | ==See Also== | |
| - | + | *[[Isocitrate dehydrogenase|Isocitrate dehydrogenase]] | |
| - | == | + | == References == |
| - | [[ | + | <references/> |
| - | [[Category: | + | __TOC__ |
| - | [[Category: Carrondo, M A | + | </StructureSection> |
| - | [[Category: Dean, A M | + | [[Category: Ecoli]] |
| - | [[Category: Goncalves, S | + | [[Category: Carrondo, M A]] |
| - | [[Category: Matias, P M | + | [[Category: Dean, A M]] |
| - | [[Category: Miller, S P | + | [[Category: Goncalves, S]] |
| + | [[Category: Matias, P M]] | ||
| + | [[Category: Miller, S P]] | ||
[[Category: Oxidative beta-decarboxylation]] | [[Category: Oxidative beta-decarboxylation]] | ||
[[Category: Oxidoreductase]] | [[Category: Oxidoreductase]] | ||
Revision as of 09:58, 4 January 2015
3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with isocitrate, magnesium(II), Adenosine 2',5'-biphosphate and ribosylnicotinamide-5'-phosphate
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