2z8y

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(New page: 200px<br /><applet load="2z8y" size="350" color="white" frame="true" align="right" spinBox="true" caption="2z8y, resolution 2.51&Aring;" /> '''Xenon-bound structur...)
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[[Image:2z8y.jpg|left|200px]]<br /><applet load="2z8y" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:2z8y.jpg|left|200px]]
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caption="2z8y, resolution 2.51&Aring;" />
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'''Xenon-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase(CODH/ACS) from Moorella thermoacetica'''<br />
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{{Structure
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|PDB= 2z8y |SIZE=350|CAPTION= <scene name='initialview01'>2z8y</scene>, resolution 2.51&Aring;
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|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>
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|LIGAND= <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</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> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
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|ACTIVITY= [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]
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|GENE=
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}}
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'''Xenon-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase(CODH/ACS) from Moorella thermoacetica'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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2Z8Y is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Moorella_thermoacetica Moorella thermoacetica] with <scene name='pdbligand=CU1:'>CU1</scene>, <scene name='pdbligand=NI:'>NI</scene>, <scene name='pdbligand=SF4:'>SF4</scene>, <scene name='pdbligand=XCC:'>XCC</scene>, <scene name='pdbligand=XE:'>XE</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Known structural/functional Sites: <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>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8Y OCA].
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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].
==Reference==
==Reference==
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=18293927 18293927]
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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]
[[Category: CO-methylating acetyl-CoA synthase]]
[[Category: CO-methylating acetyl-CoA synthase]]
[[Category: Moorella thermoacetica]]
[[Category: Moorella thermoacetica]]
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[[Category: xenon]]
[[Category: xenon]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Mar 14 09:37:51 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:53:00 2008''

Revision as of 16:53, 20 March 2008

Image:2z8y.jpg


PDB ID 2z8y

Drag the structure with the mouse to rotate
, resolution 2.51Å
Sites: , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , and
Ligands: , , , , and
Activity: CO-methylating acetyl-CoA synthase, with EC number 2.3.1.169
Coordinates: save as pdb, mmCIF, xml



Xenon-bound structure of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase(CODH/ACS) from Moorella thermoacetica


Overview

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.

About this Structure

2Z8Y is a Protein complex structure of sequences from Moorella thermoacetica. Full crystallographic information is available from OCA.

Reference

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

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