View source for 6lkz


==Crystal structure of isocitrate dehydrogenase 1 from Phaeodactylum tricornutum==
<StructureSection load='6lkz' size='340' side='right'caption='[[6lkz]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6lkz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Phaeodactylum_tricornutum Phaeodactylum tricornutum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LKZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LKZ 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]] 2.8&#8491;</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=6lkz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6lkz OCA], [https://pdbe.org/6lkz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6lkz RCSB], [https://www.ebi.ac.uk/pdbsum/6lkz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6lkz ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/B7G620_PHATC B7G620_PHATC] 
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== Publication Abstract from PubMed ==
The marine diatom Phaeodactylum tricornutum originated from a series of secondary symbiotic events and has been used as a model organism for studying diatom biology. A novel type II homodimeric isocitrate dehydrogenase from P. tricornutum (PtIDH1) was expressed, purified, and identified in detail through enzymatic characterization. Kinetic analysis showed that PtIDH1 is NAD(+)-dependent and has no detectable activity with NADP(+). The catalytic efficiency of PtIDH1 for NAD(+) is 0.16 muM(-1).s(-1) and 0.09 muM(-1).s(-1) in the presence of Mn(2+) and Mg(2+), respectively. Unlike other bacterial homodimeric NAD-IDHs, PtIDH1 activity was allosterically regulated by the isocitrate. Furthermore, the dimeric structure of PtIDH1 was determined at 2.8 A resolution, and each subunit was resolved into four domains, similar to the eukaryotic homodimeric NADP-IDH in the type II subfamily. Interestingly, a unique and novel C-terminal EF-hand domain was first defined in PtIDH1. Deletion of this domain disrupted the intact dimeric structure and activity. Mutation of the four Ca(2+)-binding sites in the EF-hand significantly reduced the calcium tolerance of PtIDH1. Thus, we suggest that the EF-hand domain could be involved in the dimerization and Ca(2+)-coordination of PtIDH1. The current report, on the first structure of type II eukaryotic NAD-IDH, provides new information for further investigation of the evolution of the IDH family.

Biochemical Characterization and Crystal Structure of a Novel NAD(+)-Dependent Isocitrate Dehydrogenase from Phaeodactylum tricornutum.,Huang SP, Zhou LC, Wen B, Wang P, Zhu GP Int J Mol Sci. 2020 Aug 18;21(16). pii: ijms21165915. doi: 10.3390/ijms21165915. PMID:32824636<ref>PMID:32824636</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6lkz" style="background-color:#fffaf0;"></div>

==See Also==
*[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]]
== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Phaeodactylum tricornutum]]
[[Category: Zhu GP]]