4ajs

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[[Image:4ajs.jpg|left|200px]]
 
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{{STRUCTURE_4ajs| PDB=4ajs | SCENE= }}
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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==
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<StructureSection load='4ajs' size='340' side='right'caption='[[4ajs]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[4ajs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. 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 [https://proteopedia.org/fgij/fg.htm?mol=4AJS FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.802&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4ajs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ajs OCA], [https://pdbe.org/4ajs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ajs RCSB], [https://www.ebi.ac.uk/pdbsum/4ajs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ajs ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/IDH_ECOLI IDH_ECOLI]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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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===
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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>
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{{ABSTRACT_PUBMED_22891681}}
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 4ajs" style="background-color:#fffaf0;"></div>
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==About this Structure==
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==See Also==
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[[4ajs]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AJS OCA].
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*[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]]
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[[Category: Escherichia coli k-12]]
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== References ==
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[[Category: Carrondo, M A.]]
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<references/>
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[[Category: Dean, A M.]]
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__TOC__
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[[Category: Goncalves, S.]]
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</StructureSection>
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[[Category: Matias, P M.]]
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[[Category: Escherichia coli K-12]]
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[[Category: Miller, S P.]]
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[[Category: Large Structures]]
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[[Category: Oxidative beta-decarboxylation]]
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[[Category: Carrondo MA]]
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[[Category: Oxidoreductase]]
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[[Category: Dean AM]]
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[[Category: Goncalves S]]
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[[Category: Matias PM]]
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[[Category: Miller SP]]

Current revision

3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with isocitrate, magnesium(II), Adenosine 2',5'-biphosphate and ribosylnicotinamide-5'-phosphate

PDB ID 4ajs

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