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3i04

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Cyanide-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica, cyanide-bound C-cluster

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 NiFe4S4 or a NiFe4S5 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 Moorella thermoacetica bound both with a substrate H2O/OH- 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 H2O/OH- 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 H2O/OH- 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.

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3i04"

Categories: Large Structures | Moorella thermoacetica | Doukov TI | Drennan CL | Kung Y

@@ Line 1: / Line 1: @@
 ==Cyanide-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica, cyanide-bound C-cluster==
-<StructureSection load='3i04' size='340' side='right' caption='[[3i04]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
+<StructureSection load='3i04' size='340' side='right'caption='[[3i04]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3i04]] is a 8 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/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"><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]] 2.15&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1mjg|1mjg]], [[3i01|3i01]]</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'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3i04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3i04 OCA], [http://pdbe.org/3i04 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3i04 RCSB], [http://www.ebi.ac.uk/pdbsum/3i04 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://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. [[http://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 ==
 [[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/i0/3i04_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/i0/3i04_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[Acetyl-CoA synthase|Acetyl-CoA synthase]]
+*[[Acetyl-CoA synthase 3D structures|Acetyl-CoA synthase 3D structures]]
-*[[Carbon monoxide dehydrogenase|Carbon monoxide dehydrogenase]]
+*[[Carbon monoxide dehydrogenase 3D structures|Carbon monoxide dehydrogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[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]]

3i04

From Proteopedia

Current revision

Cyanide-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica, cyanide-bound C-cluster

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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