3i39: Difference between revisions
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< | ==NI,FE-CODH-320 MV+CN state== | ||
<StructureSection load='3i39' size='340' side='right'caption='[[3i39]], [[Resolution|resolution]] 1.36Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3i39]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Carboxydothermus_hydrogenoformans_Z-2901 Carboxydothermus hydrogenoformans Z-2901]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I39 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I39 FirstGlance]. <br> | |||
or | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.36Å</td></tr> | ||
-- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</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=3i39 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i39 OCA], [https://pdbe.org/3i39 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i39 RCSB], [https://www.ebi.ac.uk/pdbsum/3i39 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i39 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/COOS2_CARHZ COOS2_CARHZ] CODH oxidizes carbon monoxide coupled, via CooF, to the reduction of a hydrogen cation by a hydrogenase (possibly CooH) (By similarity). | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i3/3i39_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3i39 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Carbon monoxide dehydrogenases (CODHs) catalyze the reversible oxidation of carbon monoxide with water to carbon dioxide, two protons, and two electrons. The CODHs of anaerobic microorganisms harbor a complex Ni/Fe/S-containing metal center called a C-cluster in their active site, which activates the substrates water and carbon monoxide, stabilizes an intermediary metal-carboxylate, and transiently stores the two electrons generated in the reaction. Several small molecules have been reported to inhibit carbon monoxide oxidation by CODHs, among which the cyanide anion acts as a slow binding inhibitor. Cyanide is isoelectronic to the substrate carbon monoxide, and its binding to the C-cluster has been reported to involve nickel, nickel and iron, or only iron. We report the crystal structure of CODH-II from Carboxydothermus hydrogenoformans in complex with cyanide at 1.36 A resolution. The structure reveals that cyanide binds to the C-cluster at an open coordination site completing the square-planar coordination geometry of the nickel ion. While active CODH has a water/hydroxo-ligand bound to an iron ion near nickel, in the cyanide complex the water/hydroxo-ligand is lost and iron occupies a position more close to the nickel ion. Based on the structure, we suggest that the competitive inhibitory character of cyanide originates from it obstruction of carbon monoxide binding to the nickel ion while the slow binding inhibition is due to a conformational change of the protein during which the water/hydroxo-ligand bound to iron is lost. | |||
Structural basis of cyanide inhibition of Ni, Fe-containing carbon monoxide dehydrogenase.,Jeoung JH, Dobbek H J Am Chem Soc. 2009 Jul 29;131(29):9922-3. PMID:19583208<ref>PMID:19583208</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3i39" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Carbon monoxide dehydrogenase|Carbon monoxide dehydrogenase]] | |||
*[[Carbon monoxide dehydrogenase 3D structures|Carbon monoxide dehydrogenase 3D structures]] | |||
*[[IronâÂÂsulfur proteins|IronâÂÂsulfur proteins]] | |||
== References == | |||
<references/> | |||
== | __TOC__ | ||
</StructureSection> | |||
[[Category: Carboxydothermus hydrogenoformans Z-2901]] | |||
== | [[Category: Large Structures]] | ||
< | [[Category: Dobbek H]] | ||
[[Category: | [[Category: Jeoung J-H]] | ||
[[Category: | |||
[[Category: | |||
[[Category: | |||
