6i3q

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Current revision (07:35, 1 May 2024) (edit) (undo)
 
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<StructureSection load='6i3q' size='340' side='right'caption='[[6i3q]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
<StructureSection load='6i3q' size='340' side='right'caption='[[6i3q]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6i3q]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Thioalkalivibrio_paradoxus_arh_1 Thioalkalivibrio paradoxus arh 1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5f30 5f30]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I3Q OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6I3Q FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6i3q]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thioalkalivibrio_paradoxus_ARh_1 Thioalkalivibrio paradoxus ARh 1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5f30 5f30]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I3Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I3Q FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
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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]] 1.45&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6i3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i3q OCA], [http://pdbe.org/6i3q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i3q RCSB], [http://www.ebi.ac.uk/pdbsum/6i3q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i3q ProSAT]</span></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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=6i3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i3q OCA], [https://pdbe.org/6i3q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i3q RCSB], [https://www.ebi.ac.uk/pdbsum/6i3q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i3q ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/W0DP94_9GAMM W0DP94_9GAMM]
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Biocatalytic copper centers are generally involved in the activation and reduction of dioxygen, with only few exceptions known. Here we report the discovery and characterization of a previously undescribed copper center that forms the active site of a copper-containing enzyme thiocyanate dehydrogenase (suggested EC 1.8.2.7) that was purified from the haloalkaliphilic sulfur-oxidizing bacterium of the genus Thioalkalivibrio ubiquitous in saline alkaline soda lakes. The copper cluster is formed by three copper ions located at the corners of a near-isosceles triangle and facilitates a direct thiocyanate conversion into cyanate, elemental sulfur, and two reducing equivalents without involvement of molecular oxygen. A molecular mechanism of catalysis is suggested based on high-resolution three-dimensional structures, electron paramagnetic resonance (EPR) spectroscopy, quantum mechanics/molecular mechanics (QM/MM) simulations, kinetic studies, and the results of site-directed mutagenesis.
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Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase.,Tikhonova TV, Sorokin DY, Hagen WR, Khrenova MG, Muyzer G, Rakitina TV, Shabalin IG, Trofimov AA, Tsallagov SI, Popov VO Proc Natl Acad Sci U S A. 2020 Feb 24. pii: 1922133117. doi:, 10.1073/pnas.1922133117. PMID:32094184<ref>PMID:32094184</ref>
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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 6i3q" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Thioalkalivibrio paradoxus arh 1]]
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[[Category: Thioalkalivibrio paradoxus ARh 1]]
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[[Category: Polyakov, K M]]
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[[Category: Polyakov KM]]
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[[Category: Popov, A N]]
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[[Category: Popov AN]]
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[[Category: Popov, V O]]
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[[Category: Popov VO]]
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[[Category: Tikhkonova, T V]]
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[[Category: Tikhkonova TV]]
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[[Category: Trofimov, A A]]
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[[Category: Trofimov AA]]
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[[Category: Copper center]]
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[[Category: Oxidoreductase]]
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[[Category: Thiocyanate dehydrogenase]]
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Current revision

The structure of thiocyanate dehydrogenase from Thioalkalivibrio paradoxus complex with acetate ions.

PDB ID 6i3q

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