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| | [[Image:2z8y.jpg|left|200px]] | | [[Image:2z8y.jpg|left|200px]] |
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| - | {{Structure
| + | <!-- |
| - | |PDB= 2z8y |SIZE=350|CAPTION= <scene name='initialview01'>2z8y</scene>, resolution 2.51Å
| + | The line below this paragraph, containing "STRUCTURE_2z8y", creates the "Structure Box" on the page. |
| - | |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>
| + | You may change the PDB parameter (which sets the PDB file loaded into the applet) |
| - | |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>
| + | or the SCENE parameter (which sets the initial scene displayed when the page is loaded), |
| - | |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>
| + | or leave the SCENE parameter empty for the default display. |
| - | |GENE= | + | --> |
| - | |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> | + | {{STRUCTURE_2z8y| PDB=2z8y | SCENE= }} |
| - | |RELATEDENTRY=[[1mjg|1MJG]]
| + | |
| - | |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>
| + | |
| - | }} | + | |
| | | | |
| | '''Xenon-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase(CODH/ACS) from Moorella thermoacetica''' | | '''Xenon-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase(CODH/ACS) from Moorella thermoacetica''' |
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| | [[Category: Drennan, C L.]] | | [[Category: Drennan, C L.]] |
| | [[Category: 4fe-4]] | | [[Category: 4fe-4]] |
| - | [[Category: carbon dioxide fixation]] | + | [[Category: Carbon dioxide fixation]] |
| - | [[Category: carbon monoxide (co) channel]] | + | [[Category: Clostridium thermoaceticum]] |
| - | [[Category: clostridium thermoaceticum]]
| + | [[Category: Electron transport]] |
| - | [[Category: electron transport]] | + | [[Category: Helical domain]] |
| - | [[Category: helical domain]] | + | [[Category: Metal-binding]] |
| - | [[Category: metal-binding]] | + | [[Category: Oxidoreductase]] |
| - | [[Category: nickel-copper-iron-sulfur (ni-cu-fe-s) cluster]] | + | [[Category: Oxidoreductase/transferase complex]] |
| - | [[Category: nickel-iron-sulfur (ni-fe-s) cluster]]
| + | [[Category: Rossman fold]] |
| - | [[Category: oxidoreductase]]
| + | [[Category: Transferase]] |
| - | [[Category: oxidoreductase/transferase complex]] | + | [[Category: Transport]] |
| - | [[Category: rossman fold]] | + | [[Category: Wood-ljundahl pathway]] |
| - | [[Category: transferase]] | + | [[Category: Xenon]] |
| - | [[Category: transport]] | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 20:03:10 2008'' |
| - | [[Category: wood-ljundahl pathway]] | + | |
| - | [[Category: xenon]] | + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 2 11:32:32 2008'' | + | |
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 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
Page seeded by OCA on Sun May 4 20:03:10 2008
