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| - | [[Image:2z8y.jpg|left|200px]] | |
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| - | {{Structure
| + | ==Xenon-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase(CODH/ACS) from Moorella thermoacetica== |
| - | |PDB= 2z8y |SIZE=350|CAPTION= <scene name='initialview01'>2z8y</scene>, resolution 2.51Å
| + | <StructureSection load='2z8y' size='340' side='right'caption='[[2z8y]], [[Resolution|resolution]] 2.51Å' scene=''> |
| - | |SITE= <scene name='pdbsite=AC1:Cu1+Binding+Site+For+Residue+M+950'>AC1</scene>, <scene name='pdbsite=AC2:Ni+Binding+Site+For+Residue+M+951'>AC2</scene>, <scene name='pdbsite=AC3:Cu1+Binding+Site+For+Residue+N+950'>AC3</scene>, <scene name='pdbsite=AC4:Ni+Binding+Site+For+Residue+N+951'>AC4</scene>, <scene name='pdbsite=AC5:Cu1+Binding+Site+For+Residue+O+950'>AC5</scene>, <scene name='pdbsite=AC6:Ni+Binding+Site+For+Residue+O+951'>AC6</scene>, <scene name='pdbsite=AC7:Cu1+Binding+Site+For+Residue+P+950'>AC7</scene>, <scene name='pdbsite=AC8:Ni+Binding+Site+For+Residue+P+951'>AC8</scene>, <scene name='pdbsite=AC9:Sf4+Binding+Site+For+Residue+A+700'>AC9</scene>, <scene name='pdbsite=BC1:Sf4+Binding+Site+For+Residue+A+750'>BC1</scene>, <scene name='pdbsite=BC2:Xcc+Binding+Site+For+Residue+A+800'>BC2</scene>, <scene name='pdbsite=BC3:Sf4+Binding+Site+For+Residue+B+700'>BC3</scene>, <scene name='pdbsite=BC4:Xcc+Binding+Site+For+Residue+B+800'>BC4</scene>, <scene name='pdbsite=BC5:Sf4+Binding+Site+For+Residue+C+700'>BC5</scene>, <scene name='pdbsite=BC6:Sf4+Binding+Site+For+Residue+C+750'>BC6</scene>, <scene name='pdbsite=BC7:Xcc+Binding+Site+For+Residue+C+800'>BC7</scene>, <scene name='pdbsite=BC8:Sf4+Binding+Site+For+Residue+D+700'>BC8</scene>, <scene name='pdbsite=BC9:Xcc+Binding+Site+For+Residue+D+800'>BC9</scene>, <scene name='pdbsite=CC1:Sf4+Binding+Site+For+Residue+M+900'>CC1</scene>, <scene name='pdbsite=CC2:Sf4+Binding+Site+For+Residue+N+900'>CC2</scene>, <scene name='pdbsite=CC3:Sf4+Binding+Site+For+Residue+O+900'>CC3</scene>, <scene name='pdbsite=CC4:Sf4+Binding+Site+For+Residue+P+900'>CC4</scene>, <scene name='pdbsite=CC5:Xe+Binding+Site+For+Residue+B+1001'>CC5</scene>, <scene name='pdbsite=CC6:Xe+Binding+Site+For+Residue+B+1003'>CC6</scene>, <scene name='pdbsite=CC7:Xe+Binding+Site+For+Residue+N+1008'>CC7</scene>, <scene name='pdbsite=CC8:Xe+Binding+Site+For+Residue+B+1010'>CC8</scene>, <scene name='pdbsite=CC9:Xe+Binding+Site+For+Residue+A+1001'>CC9</scene>, <scene name='pdbsite=DC1:Xe+Binding+Site+For+Residue+A+1003'>DC1</scene>, <scene name='pdbsite=DC2:Xe+Binding+Site+For+Residue+M+1008'>DC2</scene>, <scene name='pdbsite=DC3:Xe+Binding+Site+For+Residue+A+1010'>DC3</scene>, <scene name='pdbsite=DC4:Xe+Binding+Site+For+Residue+D+1001'>DC4</scene>, <scene name='pdbsite=DC5:Xe+Binding+Site+For+Residue+D+1003'>DC5</scene>, <scene name='pdbsite=DC6:Xe+Binding+Site+For+Residue+P+1009'>DC6</scene>, <scene name='pdbsite=DC7:Xe+Binding+Site+For+Residue+D+1010'>DC7</scene>, <scene name='pdbsite=DC8:Xe+Binding+Site+For+Residue+C+1001'>DC8</scene>, <scene name='pdbsite=DC9:Xe+Binding+Site+For+Residue+C+1003'>DC9</scene>, <scene name='pdbsite=EC1:Xe+Binding+Site+For+Residue+O+1006'>EC1</scene>, <scene name='pdbsite=EC2:Xe+Binding+Site+For+Residue+O+1009'>EC2</scene>, <scene name='pdbsite=EC3:Xe+Binding+Site+For+Residue+C+1010'>EC3</scene>, <scene name='pdbsite=EC4:Gol+Binding+Site+For+Residue+A+860'>EC4</scene>, <scene name='pdbsite=EC5:Gol+Binding+Site+For+Residue+A+861'>EC5</scene>, <scene name='pdbsite=EC6:Gol+Binding+Site+For+Residue+A+862'>EC6</scene>, <scene name='pdbsite=EC7:Gol+Binding+Site+For+Residue+A+863'>EC7</scene>, <scene name='pdbsite=EC8:Gol+Binding+Site+For+Residue+B+860'>EC8</scene>, <scene name='pdbsite=EC9:Gol+Binding+Site+For+Residue+B+861'>EC9</scene>, <scene name='pdbsite=FC1:Gol+Binding+Site+For+Residue+B+863'>FC1</scene>, <scene name='pdbsite=FC2:Gol+Binding+Site+For+Residue+C+860'>FC2</scene>, <scene name='pdbsite=FC3:Gol+Binding+Site+For+Residue+C+861'>FC3</scene>, <scene name='pdbsite=FC4:Gol+Binding+Site+For+Residue+D+860'>FC4</scene> and <scene name='pdbsite=FC5:Gol+Binding+Site+For+Residue+D+863'>FC5</scene>
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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>, <scene name='pdbligand=XE:XENON'>XE</scene>
| + | <table><tr><td colspan='2'>[[2z8y]] 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=2Z8Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z8Y FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/CO-methylating_acetyl-CoA_synthase CO-methylating acetyl-CoA synthase], 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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.51Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr> |
| - | |DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd01915 CODH], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam03598 CdhC], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd01917 ACS_2], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PRK09529 PRK09529]</span>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2z8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8y OCA], [https://pdbe.org/2z8y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z8y RCSB], [https://www.ebi.ac.uk/pdbsum/2z8y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z8y ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=[[1mjg|1MJG]]
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8y OCA], [http://www.ebi.ac.uk/pdbsum/2z8y PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2z8y RCSB]</span>
| + | == 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. |
| | + | == 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/z8/2z8y_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </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=2z8y ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | A fascinating feature of some bifunctional enzymes is the presence of an internal channel or tunnel to connect the multiple active sites. A channel can allow for a reaction intermediate generated at one active site to be used as a substrate at a second active site, without the need for the intermediate to leave the safety of the protein matrix. One such bifunctional enzyme is carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica (mtCODH/ACS). A key player in the global carbon cycle, CODH/ACS uses a Ni-Fe-S center called the C-cluster to reduce carbon dioxide to carbon monoxide and uses a second Ni-Fe-S center, called the A-cluster, to assemble acetyl-CoA from a methyl group, coenzyme A, and C-cluster-generated CO. mtCODH/ACS has been proposed to contain one of the longest enzyme channels (138 A long) to allow for intermolecular CO transport. Here, we report a 2.5 A resolution structure of xenon-pressurized mtCODH/ACS and examine the nature of gaseous cavities within this enzyme. We find that the cavity calculation program CAVENV accurately predicts the channels connecting the C- and A-clusters, with 17 of 19 xenon binding sites within the predicted regions. Using this X-ray data, we analyze the amino acid composition surrounding the 19 Xe sites and consider how the protein fold is utilized to carve out such an impressive interior passageway. Finally, structural comparisons of Xe-pressurized mtCODH/ACS with related enzyme structures allow us to study channel design principles, as well as consider the conformational flexibility of an enzyme that contains a cavity through its center. |
| | | | |
| - | '''Xenon-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase(CODH/ACS) from Moorella thermoacetica'''
| + | Xenon in and at the End of the Tunnel of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase(,).,Doukov TI, Blasiak LC, Seravalli J, Ragsdale SW, Drennan CL Biochemistry. 2008 Mar 18;47(11):3474-83. Epub 2008 Feb 23. PMID:18293927<ref>PMID:18293927</ref> |
| | | | |
| | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 2z8y" style="background-color:#fffaf0;"></div> |
| | | | |
| - | ==Overview== | + | ==See Also== |
| - | A fascinating feature of some bifunctional enzymes is the presence of an internal channel or tunnel to connect the multiple active sites. A channel can allow for a reaction intermediate generated at one active site to be used as a substrate at a second active site, without the need for the intermediate to leave the safety of the protein matrix. One such bifunctional enzyme is carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica (mtCODH/ACS). A key player in the global carbon cycle, CODH/ACS uses a Ni-Fe-S center called the C-cluster to reduce carbon dioxide to carbon monoxide and uses a second Ni-Fe-S center, called the A-cluster, to assemble acetyl-CoA from a methyl group, coenzyme A, and C-cluster-generated CO. mtCODH/ACS has been proposed to contain one of the longest enzyme channels (138 A long) to allow for intermolecular CO transport. Here, we report a 2.5 A resolution structure of xenon-pressurized mtCODH/ACS and examine the nature of gaseous cavities within this enzyme. We find that the cavity calculation program CAVENV accurately predicts the channels connecting the C- and A-clusters, with 17 of 19 xenon binding sites within the predicted regions. Using this X-ray data, we analyze the amino acid composition surrounding the 19 Xe sites and consider how the protein fold is utilized to carve out such an impressive interior passageway. Finally, structural comparisons of Xe-pressurized mtCODH/ACS with related enzyme structures allow us to study channel design principles, as well as consider the conformational flexibility of an enzyme that contains a cavity through its center.
| + | *[[Acetyl-CoA synthase 3D structures|Acetyl-CoA synthase 3D structures]] |
| - | | + | *[[Carbon monoxide dehydrogenase|Carbon monoxide dehydrogenase]] |
| - | ==About this Structure==
| + | *[[Carbon monoxide dehydrogenase 3D structures|Carbon monoxide dehydrogenase 3D structures]] |
| - | 2Z8Y is a [[Protein complex]] structure of sequences 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=2Z8Y OCA].
| + | *[[IronâÂÂsulfur proteins|IronâÂÂsulfur proteins]] |
| - | | + | == References == |
| - | ==Reference== | + | <references/> |
| - | Xenon in and at the End of the Tunnel of Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase(,)., Doukov TI, Blasiak LC, Seravalli J, Ragsdale SW, Drennan CL, Biochemistry. 2008 Mar 18;47(11):3474-83. Epub 2008 Feb 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18293927 18293927]
| + | __TOC__ |
| - | [[Category: CO-methylating acetyl-CoA synthase]] | + | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Moorella thermoacetica]] | | [[Category: Moorella thermoacetica]] |
| - | [[Category: Protein complex]]
| + | [[Category: Blasiak LC]] |
| - | [[Category: Blasiak, L C.]] | + | [[Category: Doukov TI]] |
| - | [[Category: Doukov, T I.]] | + | [[Category: Drennan CL]] |
| - | [[Category: Drennan, C L.]] | + | |
| - | [[Category: 4fe-4]]
| + | |
| - | [[Category: carbon dioxide fixation]]
| + | |
| - | [[Category: carbon monoxide (co) channel]]
| + | |
| - | [[Category: clostridium thermoaceticum]]
| + | |
| - | [[Category: electron transport]]
| + | |
| - | [[Category: helical domain]]
| + | |
| - | [[Category: metal-binding]]
| + | |
| - | [[Category: nickel-copper-iron-sulfur (ni-cu-fe-s) cluster]]
| + | |
| - | [[Category: nickel-iron-sulfur (ni-fe-s) cluster]]
| + | |
| - | [[Category: oxidoreductase]]
| + | |
| - | [[Category: oxidoreductase/transferase complex]]
| + | |
| - | [[Category: rossman fold]]
| + | |
| - | [[Category: transferase]]
| + | |
| - | [[Category: transport]]
| + | |
| - | [[Category: wood-ljundahl pathway]]
| + | |
| - | [[Category: xenon]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 2 11:32:32 2008''
| + | |
