7cnr: Difference between revisions
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==== | ==Crystal structure of Thermococcus kodakaraensis aconitase X (apo-form)== | ||
<StructureSection load='7cnr' size='340' side='right'caption='[[7cnr]]' scene=''> | <StructureSection load='7cnr' size='340' side='right'caption='[[7cnr]], [[Resolution|resolution]] 3.39Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br> | <table><tr><td colspan='2'>[[7cnr]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7CNR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7CNR FirstGlance]. <br> | ||
</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=7cnr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cnr OCA], [https://pdbe.org/7cnr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cnr RCSB], [https://www.ebi.ac.uk/pdbsum/7cnr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cnr ProSAT]</span></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.39Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F3S:FE3-S4+CLUSTER'>F3S</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=7cnr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7cnr OCA], [https://pdbe.org/7cnr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7cnr RCSB], [https://www.ebi.ac.uk/pdbsum/7cnr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7cnr ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q5JGJ6_THEKO Q5JGJ6_THEKO] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Aconitase superfamily members catalyze the homologous isomerization of specific substrates by sequential dehydration and hydration and contain a [4Fe-4S] cluster. However, monomeric and heterodimeric types of function unknown aconitase X (AcnX) have recently been characterized as a cis-3-hydroxy-L-proline dehydratase (AcnX(Type-I)) and mevalonate 5-phosphate dehydratase (AcnX(Type-II)), respectively. We herein elucidated the crystal structures of AcnX(Type-I) from Agrobacterium tumefaciens (AtAcnX) and AcnX(Type-II) from Thermococcus kodakarensis (TkAcnX) without a ligand and in complex with substrates. AtAcnX and TkAcnX contained the [2Fe-2S] and [3Fe-4S] clusters, respectively, conforming to UV and EPR spectroscopy analyses. The binding sites of the [Fe-S] cluster and substrate were clearlydifferent from those that were completely conserved in other aconitase enzymes; however, theoverall structural frameworks and locations of active sites were partially similar to each other.These results provide novel insights into the evolutionary scenario of the aconitase superfamilybased on the recruitment hypothesis. | |||
Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily.,Watanabe S, Murase Y, Watanabe Y, Sakurai Y, Tajima K Commun Biol. 2021 Jun 7;4(1):687. doi: 10.1038/s42003-021-02147-5. PMID:34099860<ref>PMID:34099860</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 7cnr" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Aconitase 3D structures|Aconitase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Thermococcus kodakarensis KOD1]] | ||
[[Category: Murase Y]] | |||
[[Category: Watanabe S]] | |||
[[Category: Watanabe Y]] | |||
Latest revision as of 22:30, 29 May 2024
Crystal structure of Thermococcus kodakaraensis aconitase X (apo-form)Crystal structure of Thermococcus kodakaraensis aconitase X (apo-form)
Structural highlights
FunctionPublication Abstract from PubMedAconitase superfamily members catalyze the homologous isomerization of specific substrates by sequential dehydration and hydration and contain a [4Fe-4S] cluster. However, monomeric and heterodimeric types of function unknown aconitase X (AcnX) have recently been characterized as a cis-3-hydroxy-L-proline dehydratase (AcnX(Type-I)) and mevalonate 5-phosphate dehydratase (AcnX(Type-II)), respectively. We herein elucidated the crystal structures of AcnX(Type-I) from Agrobacterium tumefaciens (AtAcnX) and AcnX(Type-II) from Thermococcus kodakarensis (TkAcnX) without a ligand and in complex with substrates. AtAcnX and TkAcnX contained the [2Fe-2S] and [3Fe-4S] clusters, respectively, conforming to UV and EPR spectroscopy analyses. The binding sites of the [Fe-S] cluster and substrate were clearlydifferent from those that were completely conserved in other aconitase enzymes; however, theoverall structural frameworks and locations of active sites were partially similar to each other.These results provide novel insights into the evolutionary scenario of the aconitase superfamilybased on the recruitment hypothesis. Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily.,Watanabe S, Murase Y, Watanabe Y, Sakurai Y, Tajima K Commun Biol. 2021 Jun 7;4(1):687. doi: 10.1038/s42003-021-02147-5. PMID:34099860[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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