6l57: Difference between revisions
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==Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with CIT , Mg and ATP binding at allosteric site.== | ==Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with CIT , Mg and ATP binding at allosteric site.== | ||
<StructureSection load='6l57' size='340' side='right'caption='[[6l57]]' scene=''> | <StructureSection load='6l57' size='340' side='right'caption='[[6l57]], [[Resolution|resolution]] 2.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L57 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6l57]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6L57 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6L57 FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.302Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6l57 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6l57 OCA], [https://pdbe.org/6l57 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6l57 RCSB], [https://www.ebi.ac.uk/pdbsum/6l57 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6l57 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/IDH3A_HUMAN IDH3A_HUMAN] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Human NAD-dependent isocitrate dehydrogenase (NAD-IDH) is responsible for the catalytic conversion of isocitrate into alpha-ketoglutarate in the Krebs cycle. This enzyme exists as the alpha2betagamma heterotetramer composed of the alphabeta and alphagamma heterodimers. Our previous biochemical data showed that the alphagamma heterodimer and the holoenzyme can be activated by low concentrations of ATP but inhibited by high concentrations of ATP; however, the molecular mechanism was unknown. Here, we report the crystal structures of the alphagamma heterodimer with ATP binding only to the allosteric site (alpha(Mg)gamma(Mg+CIT+ATP)) and to both the allosteric site and the active site (alpha(Mg+ATP)gamma(Mg+CIT+ATP)). Structural data show that ATP at low concentrations can mimic ADP to bind to the allosteric site, which stabilizes CIT binding and leads the enzyme to adopt an active conformation, revealing why the enzyme can be activated by low concentrations of ATP. On the other hand, at high concentrations ATP is competitive with NAD for binding to the catalytic site. In addition, our biochemical data show that high concentrations of ATP promote the formation of metal ion-ATP chelates. This reduces the concentration of free metal ion available for the catalytic reaction, and thus further inhibits the enzymatic activity. The combination of these two effects accounts for the inhibition of the enzyme at high concentrations of ATP. Taken together, our structural and biochemical data reveal the molecular mechanism for the dual regulatory roles of ATP on the alphagamma heterodimer of human NAD-IDH. | |||
Molecular mechanism of the dual regulatory roles of ATP on the alphagamma heterodimer of human NAD-dependent isocitrate dehydrogenase.,Sun P, Bai T, Ma T, Ding J Sci Rep. 2020 Apr 10;10(1):6225. doi: 10.1038/s41598-020-63425-6. PMID:32277159<ref>PMID:32277159</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6l57" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Homo sapiens]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Ding J]] | [[Category: Ding J]] | ||
[[Category: Sun P]] | [[Category: Sun P]] | ||