1su8
From Proteopedia
(New page: 200px<br /><applet load="1su8" size="450" color="white" frame="true" align="right" spinBox="true" caption="1su8, resolution 1.10Å" /> '''Carbon Monoxide Indu...) |
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| - | [[Image:1su8.gif|left|200px]]<br /><applet load="1su8" size=" | + | [[Image:1su8.gif|left|200px]]<br /><applet load="1su8" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1su8, resolution 1.10Å" /> | caption="1su8, resolution 1.10Å" /> | ||
'''Carbon Monoxide Induced Decomposition of the Active Site [Ni-4Fe-5S] Cluster of CO Dehydrogenase'''<br /> | '''Carbon Monoxide Induced Decomposition of the Active Site [Ni-4Fe-5S] Cluster of CO Dehydrogenase'''<br /> | ||
==Overview== | ==Overview== | ||
| - | During the past two years, crystal structures of Cu- and Mo-containing | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 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 SF4, FES and NFS as [http://en.wikipedia.org/wiki/ligands ligands]. This structure | + | 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]. |
==Reference== | ==Reference== | ||
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[[Category: nickel]] | [[Category: nickel]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:05:15 2008'' |
Revision as of 13:05, 21 February 2008
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Carbon Monoxide Induced Decomposition of the Active Site [Ni-4Fe-5S] Cluster of CO Dehydrogenase
Overview
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.
About this Structure
1SU8 is a Single protein structure of sequence from Carboxydothermus hydrogenoformans with , and as ligands. This structure supersedes the now removed PDB entry 1JJY. Active as Carbon-monoxide dehydrogenase (acceptor), with EC number 1.2.99.2 Full crystallographic information is available from OCA.
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:15113209
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