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| | == Structural highlights == | | == Structural highlights == |
| | <table><tr><td colspan='2'>[[3i04]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Moorella_thermoacetica Moorella thermoacetica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I04 FirstGlance]. <br> | | <table><tr><td colspan='2'>[[3i04]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Moorella_thermoacetica Moorella thermoacetica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3I04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3I04 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=XCC:FE(4)-NI(1)-S(4)+CLUSTER'>XCC</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]] 2.15Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1mjg|1mjg]], [[3i01|3i01]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=XCC:FE(4)-NI(1)-S(4)+CLUSTER'>XCC</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Transferase Transferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.169 2.3.1.169] </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=3i04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i04 OCA], [https://pdbe.org/3i04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i04 RCSB], [https://www.ebi.ac.uk/pdbsum/3i04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i04 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=3i04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i04 OCA], [https://pdbe.org/3i04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3i04 RCSB], [https://www.ebi.ac.uk/pdbsum/3i04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3i04 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/DCMB_MOOTH DCMB_MOOTH]] The beta subunit (this protein) generates CO from CO(2), while the alpha subunit combines the CO with CoA and a methyl group to form acetyl-CoA. The methyl group, which is incorporated into acetyl-CoA, is transferred to the alpha subunit by a corrinoid iron-sulfur protein. [[https://www.uniprot.org/uniprot/DCMA_MOOTH DCMA_MOOTH]] The beta subunit generates CO from CO(2), while the alpha subunit (this protein) combines the CO with CoA and a methyl group to form acetyl-CoA. The methyl group, which is incorporated into acetyl-CoA, is transferred to the alpha subunit by a corrinoid iron-sulfur protein.
| + | [https://www.uniprot.org/uniprot/DCMB_MOOTH DCMB_MOOTH] The beta subunit (this protein) generates CO from CO(2), while the alpha subunit combines the CO with CoA and a methyl group to form acetyl-CoA. The methyl group, which is incorporated into acetyl-CoA, is transferred to the alpha subunit by a corrinoid iron-sulfur protein. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| | [[Category: Moorella thermoacetica]] | | [[Category: Moorella thermoacetica]] |
| - | [[Category: Transferase]]
| + | [[Category: Doukov TI]] |
| - | [[Category: Doukov, T I]] | + | [[Category: Drennan CL]] |
| - | [[Category: Drennan, C L]] | + | [[Category: Kung Y]] |
| - | [[Category: Kung, Y]] | + | |
| - | [[Category: Carbon dioxide fixation]]
| + | |
| - | [[Category: Electron transport]]
| + | |
| - | [[Category: Iron]]
| + | |
| - | [[Category: Iron-sulfur]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Nickel]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Oxidoreductase-transferase complex]]
| + | |
| - | [[Category: Protein-protein complex]]
| + | |
| - | [[Category: Transport]]
| + | |
| Structural highlights
3i04 is a 8 chain structure with sequence from Moorella thermoacetica. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.15Å |
| Ligands: | , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
DCMB_MOOTH The beta subunit (this protein) generates CO from CO(2), while the alpha subunit combines the CO with CoA and a methyl group to form acetyl-CoA. The methyl group, which is incorporated into acetyl-CoA, is transferred to the alpha subunit by a corrinoid iron-sulfur protein.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Nickel-containing carbon monoxide dehydrogenases (CODHs) reversibly catalyze the oxidation of carbon monoxide to carbon dioxide and are of vital importance in the global carbon cycle. The unusual catalytic CODH C-cluster has been crystallographically characterized as either a NiFe<sub>4</sub>S<sub>4</sub> or a NiFe<sub>4</sub>S<sub>5</sub> metal center, the latter containing a fifth, additional sulfide that bridges Ni and a unique Fe site. To determine whether this bridging sulfide is catalytically relevant and to further explore the mechanism of the C-cluster, we obtained crystal structures of the 310 kDa bifunctional CODH/acetyl-CoA synthase complex from <i>Moorella thermoacetica</i> bound both with a substrate H<sub>2</sub>O/OH<sup>-</sup> molecule and a cyanide inhibitor. X-ray diffraction data were collected from native crystals and from identical crystals soaked in a solution containing potassium cyanide. In both structures, the substrate H<sub>2</sub>O/OH<sup>-</sup> molecule exhibits binding to the unique Fe site of the C-cluster. We also observe cyanide binding in a bent conformation to Ni of the C-cluster, adjacent the substrate H<sub>2</sub>O/OH<sup>-</sup> molecule. Importantly, the bridging sulfide is not present in either structure. As these forms of the C-cluster represent the coordination environment immediately before the reaction takes place, our findings do not support a fifth, bridging sulfide playing a catalytic role in the enzyme mechanism. The crystal structures presented here, along with recent structures of CODHs from other organisms, have led us towards a unified mechanism for CO oxidation by the C-cluster, the catalytic center of an environmentally important enzyme.
Crystallographic snapshots of cyanide- and water-bound C-clusters from bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase.,Kung Y, Doukov TI, Seravalli J, Ragsdale SW, Drennan CL Biochemistry. 2009 Jul 7. PMID:19583207[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Kung Y, Doukov TI, Seravalli J, Ragsdale SW, Drennan CL. Crystallographic snapshots of cyanide- and water-bound C-clusters from bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase. Biochemistry. 2009 Jul 7. PMID:19583207 doi:10.1021/bi900574h
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