4aj3: Difference between revisions

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[[Image:4aj3.jpg|left|200px]]


{{STRUCTURE_4aj3| PDB=4aj3 | SCENE= }}
==3D structure of E. coli Isocitrate Dehydrogenase in complex with Isocitrate, calcium(II) and NADP - The pseudo-Michaelis complex==
<StructureSection load='4aj3' size='340' side='right'caption='[[4aj3]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4aj3]] 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=4AJ3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AJ3 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ICT:ISOCITRIC+ACID'>ICT</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4aj3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aj3 OCA], [https://pdbe.org/4aj3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4aj3 RCSB], [https://www.ebi.ac.uk/pdbsum/4aj3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4aj3 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/IDH_ECOLI IDH_ECOLI]
<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.


===3D structure of E. coli Isocitrate Dehydrogenase in complex with Isocitrate, calcium(II) and NADP - The pseudo-Michaelis complex===
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>


{{ABSTRACT_PUBMED_22891681}}
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4aj3" style="background-color:#fffaf0;"></div>


==About this Structure==
==See Also==
[[4aj3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lepidoptera_sp._bold:aaa8691 Lepidoptera sp. bold:aaa8691]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AJ3 OCA].
*[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]]
[[Category: Lepidoptera sp. bold:aaa8691]]
== References ==
[[Category: Carrondo, M A.]]
<references/>
[[Category: Dean, A M.]]
__TOC__
[[Category: Goncalves, S.]]
</StructureSection>
[[Category: Matias, P M.]]
[[Category: Escherichia coli K-12]]
[[Category: Miller, S P.]]
[[Category: Large Structures]]
[[Category: Oxidative beta-decarboxylation]]
[[Category: Carrondo MA]]
[[Category: Oxidoreductase]]
[[Category: Dean AM]]
[[Category: Goncalves S]]
[[Category: Matias PM]]
[[Category: Miller SP]]
Retrieved from "https://proteopedia.org/4aj3"