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1su8

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[[Image:1su8.gif|left|200px]]<br /><applet load="1su8" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1su8, resolution 1.10&Aring;" />
 
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'''Carbon Monoxide Induced Decomposition of the Active Site [Ni-4Fe-5S] Cluster of CO Dehydrogenase'''<br />
 
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==Overview==
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==Carbon Monoxide Induced Decomposition of the Active Site [Ni-4Fe-5S] Cluster of CO Dehydrogenase==
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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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<StructureSection load='1su8' size='340' side='right'caption='[[1su8]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1su8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Carboxydothermus_hydrogenoformans Carboxydothermus hydrogenoformans]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1jjy 1jjy]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SU8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SU8 FirstGlance]. <br>
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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]] 1.1&#8491;</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>
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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=1su8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1su8 OCA], [https://pdbe.org/1su8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1su8 RCSB], [https://www.ebi.ac.uk/pdbsum/1su8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1su8 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/su/1su8_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1su8 ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1SU8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Carboxydothermus_hydrogenoformans Carboxydothermus hydrogenoformans] with <scene name='pdbligand=SF4:'>SF4</scene>, <scene name='pdbligand=FES:'>FES</scene> and <scene name='pdbligand=NFS:'>NFS</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 1JJY. Active as [http://en.wikipedia.org/wiki/Carbon-monoxide_dehydrogenase_(acceptor) Carbon-monoxide dehydrogenase (acceptor)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.99.2 1.2.99.2] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SU8 OCA].
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*[[Carbon monoxide dehydrogenase 3D structures|Carbon monoxide dehydrogenase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=15113209 15113209]
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[[Category: Carbon-monoxide dehydrogenase (acceptor)]]
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[[Category: Carboxydothermus hydrogenoformans]]
[[Category: Carboxydothermus hydrogenoformans]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Dobbek, H.]]
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[[Category: Dobbek H]]
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[[Category: Liss, J.]]
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[[Category: Liss J]]
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[[Category: Meyer, O.]]
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[[Category: Meyer O]]
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[[Category: Svetlitchnyi, V.]]
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[[Category: Svetlitchnyi V]]
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[[Category: FES]]
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[[Category: NFS]]
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[[Category: SF4]]
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[[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 Thu Feb 21 15:05:15 2008''
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Current revision

Carbon Monoxide Induced Decomposition of the Active Site [Ni-4Fe-5S] Cluster of CO Dehydrogenase

PDB ID 1su8

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