1su8: Difference between revisions

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<StructureSection load='1su8' size='340' side='right'caption='[[1su8]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
<StructureSection load='1su8' size='340' side='right'caption='[[1su8]], [[Resolution|resolution]] 1.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1su8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_baa-161 Atcc baa-161]. 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>
<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>
</td></tr><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>
</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>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1su6|1su6]], [[1su7|1su7]], [[1suf|1suf]]</div></td></tr>
<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>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Carbon-monoxide_dehydrogenase_(acceptor) Carbon-monoxide dehydrogenase (acceptor)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.99.2 1.2.99.2] </span></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=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>
<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>
</table>
</table>
== Function ==
== 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).  
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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].
</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>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:15113209<ref>PMID:15113209</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1su8" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Carbon monoxide dehydrogenase 3D structures|Carbon monoxide dehydrogenase 3D structures]]
*[[Carbon monoxide dehydrogenase 3D structures|Carbon monoxide dehydrogenase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc baa-161]]
[[Category: Carboxydothermus hydrogenoformans]]
[[Category: Large Structures]]
[[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]]
[[Category: Cluster c]]
[[Category: Codh]]
[[Category: Nickel]]
[[Category: Oxidoreductase]]

Revision as of 08:33, 14 February 2024

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

1su8, resolution 1.10Å

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