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| - | [[Image:1suf.jpg|left|200px]] | |
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| - | <!-- | + | ==Carbon Monoxide Dehydrogenase from Carboxydothermus hydrogenoformans-Inactive state== |
| - | The line below this paragraph, containing "STRUCTURE_1suf", creates the "Structure Box" on the page.
| + | <StructureSection load='1suf' size='340' side='right'caption='[[1suf]], [[Resolution|resolution]] 1.15Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[1suf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Carboxydothermus_hydrogenoformans Carboxydothermus hydrogenoformans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SUF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SUF FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.15Å</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=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=NFS:FE(4)-NI(1)-S(5)+CLUSTER'>NFS</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr> |
| - | {{STRUCTURE_1suf| PDB=1suf | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1suf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1suf OCA], [https://pdbe.org/1suf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1suf RCSB], [https://www.ebi.ac.uk/pdbsum/1suf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1suf 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/su/1suf_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1suf ConSurf]. |
| | + | <div style="clear:both"></div> |
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| - | '''Carbon Monoxide Dehydrogenase from Carboxydothermus hydrogenoformans-Inactive state'''
| + | ==See Also== |
| - | | + | *[[Carbon monoxide dehydrogenase 3D structures|Carbon monoxide dehydrogenase 3D structures]] |
| - | | + | __TOC__ |
| - | ==Overview== | + | </StructureSection> |
| - | During the past two years, crystal structures of Cu- and Mo-containing carbon monoxide dehydrogenases (CODHs) and Ni- and Fe-containing CODHs have been reported. The active site of CODHs from anaerobic bacteria (cluster C) is composed of Ni, Fe, and S for which crystallographic studies of the enzymes from Carboxydothermus hydrogenoformans, Rhodospirillum rubrum, and Moorella thermoaceticarevealed structural similarities in the overall protein fold but showed substantial differences in the essential Ni coordination environment. The [Ni-4Fe-5S] cluster C in the fully catalytically competent dithionite-reduced CODH II from C. hydrogenoformans (CODHII(Ch)) at 1.6 A resolution contains a characteristic mu(2)-sulfido ligand between Ni and Fe1, resulting in a square-planar ligand arrangement with four S-ligands at the Ni ion. In contrast, the [Ni-4Fe-4S] clusters C in CO-treated CODH from R. rubrum resolved at 2.8 A and in CO-treated acetyl-CoA synthase/CODH complex from M. thermoacetica at 2.2 and 1.9 A resolution, respectively, do not contain the mu(2)-sulfido ligand between Ni and Fe1 and display dissimilar geometries at the Ni ion. The [Ni-4Fe-4S] cluster is composed of a cubane [Ni-3Fe-4S] cluster linked to a mononuclear Fe site. The described coordination geometries of the Ni ion in the [Ni-4Fe-4S] cluster of R. rubrum and M. thermoacetica deviate from the square-planar ligand geometry in the [Ni-4Fe-5S] cluster C of CODHII(Ch). In addition, the latter was converted into a [Ni-4Fe-4S] cluster under specific conditions. The objective of this study was to elucidate the relationship between the structure of cluster C in CODHII(Ch) and the functionality of the protein. We have determined the CO oxidation activity of CODHII(Ch) under different conditions of crystallization, prepared crystals of the enzyme in the presence of dithiothreitol or dithionite as reducing agents under an atmosphere of N(2) or CO, and solved the corresponding structures at 1.1 to 1.6 A resolutions. Fully active CODHII(Ch) obtained after incubation of the enzyme with dithionite under N(2) revealed the [Ni-4Fe-5S] cluster. Short treatment of the enzyme with CO in the presence of dithiothreitol resulted in a catalytically competent CODHII(Ch) with a CO-reduced [Ni-4Fe-5S] cluster, but a prolonged treatment with CO caused the loss of CO-oxidizing activity and revealed a [Ni-4Fe-4S] cluster, which did not contain a mu(2)-S. These data suggest that the [Ni-4Fe-4S] cluster of CODHII(Ch) is an inactivated decomposition product originating from the [Ni-4Fe-5S] cluster.
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| - | ==About this Structure==
| + | |
| - | 1SUF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Carboxydothermus_hydrogenoformans Carboxydothermus hydrogenoformans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SUF OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Carbon monoxide induced decomposition of the active site [Ni-4Fe-5S] cluster of CO dehydrogenase., Dobbek H, Svetlitchnyi V, Liss J, Meyer O, J Am Chem Soc. 2004 May 5;126(17):5382-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15113209 15113209]
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| | [[Category: Carboxydothermus hydrogenoformans]] | | [[Category: Carboxydothermus hydrogenoformans]] |
| - | [[Category: Single protein]] | + | [[Category: Large Structures]] |
| - | [[Category: Dobbek, H.]] | + | [[Category: Dobbek H]] |
| - | [[Category: Liss, J.]] | + | [[Category: Liss J]] |
| - | [[Category: Meyer, O.]] | + | [[Category: Meyer O]] |
| - | [[Category: Svetlitchnyi, V.]] | + | [[Category: Svetlitchnyi V]] |
| - | [[Category: Carbon monoxide dehydrogenase]]
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| - | [[Category: Cluster c]]
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| - | [[Category: Codh]]
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| - | [[Category: Nickel]]
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| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 09:08:51 2008''
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