Sandbox Reserved 496: Difference between revisions

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== '''Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase (CODH/ACS)''' ==

=== '''Introduction''' ===

----

Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is a bifunctional protein which acts as both an [http://en.wikipedia.org/wiki/Oxidoreductase oxidoreductase] and a [http://en.wikipedia.org/wiki/Transferase transferase] by reducing carbon dioxide to carbon monoxide (or the reverse oxidation of carbon monoxide to carbon dioxide) and then catalyzing the synthesis of [http://en.wikipedia.org/wiki/Acetyl-CoA acetyl-CoA] from carbon monoxide, coenzyme A, and the methyl group of an corrinoid iron-sulfur protein. This enzyme plays a key role in the Wood-Ljungdahl pathway which is used by anaerobic, [http://en.wikipedia.org/wiki/Autotroph autotrophic] bacteria such as ''Moorella thermoacetica'' (f. ''Clostridium thermoaceticum'') and ''Clostridium ljungdahlii'' for gaseous carbon fixation. End products of the Wood-Ljungdahl pathway include cell biomass, acids (ex. acetate and butyrate), and alcohols (ex. ethanol and butanol) – all of which derive from acetyl-CoA. The Wood-Ljungdahl pathway is also the most energetically favorable carbon fixation pathway, but its use is confined to only obligate, anaerobic species <ref name="Berg">PMID:20453874</ref>. Since the discovery of the Wood-Ljungdahl pathway in the early 1980’s, significant effort has been put into trying to characterize the substrate binding activity of CODH/ACS with the ''M. thermoacetica'' protein used as the model in most case studies <ref name="CN">PMID:19583207</ref>. However, little progress was made in defining the exact structure of the protein with crystal structures until the 2000’s. Several reasons why CODH/ACS has received so much attention include the fact that it contains highly disputed metalloclusters, its use of biological organometallic intermediates in reactions, and its contribution to reducing environmental pollutants <ref>PMID: 11841199</ref> <ref>PMID: 11848835</ref>.

Similar bacteria which harbor monofunctional CODH enzymes include the autotrophs ''Rhodosprillum rubrum'' and ''Carboxydothermus hydrogenoformans'' <ref name="Cu">PMID:12386327</ref>. In addition, a variation on CODH/ACS termed CODH-containing acetyl-CoA decarboxylase/synthase is found in methanogenic archea and decomposes acetyl-CoA to carbon dioxide and methane <ref>PMID: 18621675</ref>.

PDB codes for the ''M. thermoacetica'' CODH/ACS enzyme are: 1MJG <ref>1MJG. [http://dx.doi.org/10.2210/pdb1mjg/pdb DOI:10.2210/pdb1mjg/pdb]</ref> <scene name='Sandbox_Reserved_496/Codh_acs/1'>(orginial scene)</scene>, 1OAO <ref>1OAO. [http://dx.doi.org/10.2210/pdb1oao/pdb DOI:10.2210/pdb1oao/pdb]</ref>, 2Z8Y <ref>2Z8Y. [http://dx.doi.org/10.2210/pdb2z8y/pdb DOI:10.2210/pdb2z8y/pdb]</ref>, 3I01 <ref>3I01. [http://dx.doi.org/10.2210/pdb3i01/pdb DOI:10.2210/pdb3i01/pdb]</ref>, and 3I04 <ref>3I04. [http://dx.doi.org/10.2210/pdb3i04/pdb DOI:10.2210/pdb3i04/pdb]</ref>.

==='''Structure'''===

----

The CODH/ACS enzyme from ''M. thermoacetica'' is an <scene name='Sandbox_Reserved_496/Codh_acs_tetramer/2'>α2β2 tetramer</scene> with seven metalloclusters. Each 674 residue <scene name='Sandbox_Reserved_496/Beta_subunits/2'>β subunit </scene> carries out CODH activity, while each 729 residue <scene name='Sandbox_Reserved_496/Alpha_subunits/1'>α subunit</scene> is responsible for ACS activity. From the N-terminus to C-terminus, <scene name='Sandbox_Reserved_496/Beta_secondary/1'> β subunit domains</scene> are as follows: an α-helical domain (residues 1-257) followed by two α/β Rossmann-like domains (residues 262-458 and 463-674). The β subunit has 57% helical and 9% β-sheet character with 31 helices and 15 β-strands. The <scene name='Sandbox_Reserved_496/Alpha_secondary/1'>α subunit is also comprised of three domains</scene>, two with α+β folds and a third with a helical region (residues 1-154) at the N-terminus of a Rossmann (six-stranded α/β) fold (residues 155-316) which is similar to a portion of the β subunit structure <ref name="Cu"/> <ref name="Xe">PMID:18293927</ref>. Overall, the α subunit has 50% helical and 14% β-sheet character with 36 helices and 22 β-strands.

<scene name='Sandbox_Reserved_496/Beta_metalloclusters/1'>Five of the metalloclusters</scene> ('''two B-''', '''two C-''', and '''one D-cluster''') are located in the β2 portion of the protein with a B- and C-cluster in each β subunit and the sole D-cluster bridging the two subunits. The B- and D-clusters consist of [Fe4S4] centers that serve to transfer electrons. As the active site in each β subunit where CODH activity occurs, the <scene name='Sandbox_Reserved_496/Beta_c_cluster/2'>C-clusters are composed of a Fe-[NiFe3S4] cage </scene> with the unique Fe coordinated by a bridging sulfur ion, His283, and Cys317 <ref name="Zn">PMID:12627225</ref>. The B- and D-clusters are positioned in relation to the α-helical domain of the β subunit, while the C-clusters are aligned through interactions with both Rossmann-like domains <ref name="Xe"/>. A ligand binding study with the native CODH/ACS structure and with cyanide used as competitive inhibitor for CO showed that H2O/OH- binds the C-cluster at the unique Fe and CO binds the C-cluster at the Ni ion <ref name="CN"/>.

The remaining two metalloclusters (both A-clusters) are located in the two α subunits of the CODH/ACS protein. As the active site of ACS activity in each α subunit, the A-clusters are composed of a [Fe4S4] center bridged to a binuclear site. There is some debate regarding the metal ions present in the binuclear site; either <scene name='Sandbox_Reserved_496/Alpha_a_cluster/1'>both A-clusters are [Fe4S4]-Cu-Ni</scene> <ref name="Cu"/> or one A-cluster is <scene name='Sandbox_Reserved_496/A_cluster_ni_ni/1'>[Fe4S4]-Ni-Ni</scene> while the other is <scene name='Sandbox_Reserved_496/A_cluster_zn_ni/1'>[Fe4S4]-Zn-Ni</scene> <ref name="Zn"/>. The [Fe4S4] center is coordinated by Cys506, Cys509, Cys518, and Cys528 with Cys509 also forming the bridge between the [Fe4S4] and the [http://en.wikipedia.org/wiki/Proximal#Proximal_and_distal proximal] metal ion. Furthermore, the distal metal ion is coordinated by Cys595, Gly596, and Cys597 with Cys595 and Cys597 also connecting the distal and the proximal metal ions. Only the [Fe4S4]-Ni-Ni A-cluster is in an open conformation, the other two site types with Cu or Zn as the proximal ion are in closed form.

Another characteristic feature of CODH/ACS is a 138Å long <scene name='Sandbox_Reserved_496/Codh_acs_hydrophilic/1'>hydrophobic tunnel</scene> that connects the C- and A-clusters. The cavity network formed by the hydrophobic tunnel is an S-shaped pore from C-cluster to C-cluster with two long branches that lead from the “S” to each A-cluster. As the tunnel runs along nearly the full length of the protein, it enables the intramolecular diffusion of CO from the CODH active sites to the ACS active sites <ref name="Cu"/>.

X-ray crystallography methods were used to determine the structure of CODH/ACS from ''M. thermoacetica''. Crystals were formed by means of sitting drop vapor diffusion. Both molecular replacement (using the CODH structure of ''R. rubrum'' <ref name="Cu"/> and ''C. hydrogenoformans'' <ref name="Zn"/>) and multiple-wavelength anomalous dispersion (MAD) methods were used to solve the structure’s diffraction pattern. Resolution of the structures at the highest resolution shell ranges from 2.5Å to 1.9Å.

==='''Mechanism of Action'''===

----

[[Image:A_cluster_1.JPG|frame|Proposed mechanism 1 for ACS activity with Cu-Ni ions in the binuclear site of the A-cluster. <ref name="Cu"/>]]

'''β subunit reactions'''

C-cluster (CODH activity): CO2 + 2H+ + 2e- ↔ CO + H2O

B- and D-clusters: electron transfer

'''α subunit reactions'''

A-cluster (ACS activity): CH3-Co(III)-CFeSP + CO + HSCoA ↔ CH3-CO-SCoA + Co(I)-CFeSP + H+

There are two proposed mechanisms for the catalytic action of the A-cluster: mechanism 1 uses Cu-Ni ions in the binuclear site while mechanism 2 uses Ni-Ni ions.

Mechanism 1 suggests that CO created at the C-cluster travels through the hydrophobic tunnel and binds to Cu. Next, the A-cluster switches to an open corrinoid conformation so that the methyl group may be transferred from the corrinoid iron-sulfur protein to the distal Ni ion of the active site. The cluster reverts back to a solvent protected, closed form to generate the acetyl intermediate, and then reopens to allow HSCoA to bind. HSCoA likely binds in the large cavity between the three domains of the α subunit where six Arg residues and Trp418 coincide. Finally, HSCoA is deprotonated and acetylated to form acetyl-CoA <ref name="Cu"/>.

[[Image:A_cluster_2.JPG|frame|Proposed mechanism 2 for ACS activity with Ni-Ni ions in the binuclear site of the A-cluster. <ref name="Zn"/>]]

~~'''Cholix Toxin''' named also CT, is a protein toxin~~ that ~~uses ADP-ribosyltransferases~~ to ~~modify target proteins in human cells~~. The ~~mono-ADP~~-~~ribosyltransferase toxins are bacterial virulence factors that are believed~~ to be a ~~factor in many disease states in animals plants~~ as ~~well even humans~~. ~~For a list~~ of ~~various~~ and ~~other similar toxins see [[Toxins]]~~.

Mechanism 2 proposes that CO binds to the proximal Ni ion after exiting the tunnel. The A-cluster then changes from the closed to the open conformation which closes the hydrophobic CO tunnel and provides a site for methyl group binding on the proximal Ni as it transitions from Ni(0) to Ni(II). Next, the bound CO inserts into the Ni-CH3 bond to produce an acetyl intermediate. Lastly, deprotonated CoA-S- attacks the carbonyl carbon of the acetyl group to produce acetyl-CoA and the proximal Ni is reduced back to Ni(0) <ref name="Zn"/>. Note that this mechanism differs from the former by binding both CO and CH3 to the proximal metal ion and also the A-cluster stays open between methylation and CoA acetylation.

<~~Structure load='569B' size='300' color='white' frame='true' align='right' caption~~=~~'testcaption'~~ />

[[Image:C_cluster.JPG|frame|Proposed mechanism for CODH activity in the C-cluster. <ref name="CN"/>]]

In the proposed catalytic action of the C-cluster, CO first binds the Ni ion followed by deprotonation of the Fe bound water to yield a reactive hydroxide which promotes nucleophilic attack of CO by the hydroxide. Next, the Ni-COOH intermediate is deprotonated to Ni-COO- which allows release of CO2 as the C-cluster is reduced to a new redox state. Then, electrons are shuttled between the B- and D-clusters to reoxidize the C-cluster to its original redox state <ref name="CN"/>. This catalytic cycle is of course operated in reverse to reduce CO2 to CO and allow subsequent production of acetyl-CoA .

==='''Possible Applications'''===

----

Since CODH/ACS consumes CO2 it plays a direct part in the reduction of greenhouse gases by converting CO2 into an intermediate which can transformed into more desirable products such as alcohols and acids. A novel application in which CODH/ACS plays a role is the production of bioethanol from renewable natural resources such as wood, grasses, and agricultural residues (ex. corn stover). In this process, the biomass undergoes [http://en.wikipedia.org/wiki/Gasification gasification] to yield CO, CO2, and H2. The gases are subsequently fed to bacterial reactor systems containing organisms which utilize the Wood-Ljungdahl pathway and thus produce ethanol. The main goal is to produce a renewable energy source that may be used as an alternative to petroleum. However, at this time, the flux of carbon through the Wood-Ljungdahl pathway does not tend to favor ethanol production so much work remains to be done in this area. On the other hand, the Wood-Ljungdahl pathway does produce significant levels of acetic acid, and to this extent, the pathway is considered a biological equivalent to the [http://en.wikipedia.org/wiki/Monsanto_process Monsanto process] for industrial acetic acid production <ref name="Berg"/>. Roughly 10% of the total biological acetic acid production is attributable to anaerobic, autotrophic bacteria which possess CODH/ACS enzymes.

== ~~Cholix Toxin from~~ ''~~Vibrio Cholerae~~ ''==

==='''References'''===

The [http://en.wikipedia.org/wiki/Crystal_structure crystal structure] of the [http://en.wikipedia.org/wiki/Proteolysis proteolytically] activated monomeric form of Cyt2Ba was determined at 2.1Å resolution. It consists of a single domain of <~~scene name='Cyt2Ba/Alpha_beta~~/5'>~~α/β</scene> architecture with a <scene name='Cyt2Ba/Beta/2'>β~~-~~sheet</scene> (yellow) surrounded by 2 <scene name='Cyt2Ba/Alpha/2'>α~~-~~helical</scene> layers (red) forming a cytolysin fold.~~

----

--[[User:Rachel Slivka|Rachel Slivka]]

Sandbox Reserved 496: Difference between revisions

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-'''Bold text'''<!-- PLEASE DO NOT DELETE THIS TEMPLATE -->
+|'''Bold text'''
+'''DO NOT DELETE UNTIL AFTER JULY 1, 2012.'''
+<!-- PLEASE DO NOT DELETE THIS TEMPLATE -->
 {{Sandbox_Reserved_Robert_B_Rose_1}}
 <!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
+== '''Bifunctional Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase (CODH/ACS)''' ==
+<Structure load='1mjg' size='400' frame='true' align='right' caption='Carbon monoxide dehydrogenase/acetyl-CoA synthase asymmetric unit containing two α2β2 tetramers.' scene='Insert optional scene name here' />
+=== '''Introduction''' ===
+----
+Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is a bifunctional protein which acts as both an [http://en.wikipedia.org/wiki/Oxidoreductase oxidoreductase] and a [http://en.wikipedia.org/wiki/Transferase transferase] by reducing carbon dioxide to carbon monoxide (or the reverse oxidation of carbon monoxide to carbon dioxide) and then catalyzing the synthesis of [http://en.wikipedia.org/wiki/Acetyl-CoA acetyl-CoA] from carbon monoxide, coenzyme A, and the methyl group of an corrinoid iron-sulfur protein.  This enzyme plays a key role in the Wood-Ljungdahl pathway which is used by anaerobic, [http://en.wikipedia.org/wiki/Autotroph autotrophic] bacteria such as ''Moorella thermoacetica''  (f. ''Clostridium thermoaceticum'') and ''Clostridium ljungdahlii'' for gaseous carbon fixation.  End products of the Wood-Ljungdahl pathway include cell biomass, acids (ex. acetate and butyrate), and alcohols (ex. ethanol and butanol) – all of which derive from acetyl-CoA.  The Wood-Ljungdahl pathway is also the most energetically favorable carbon fixation pathway, but its use is confined to only obligate, anaerobic species <ref name="Berg">PMID:20453874</ref>.  Since the discovery of the Wood-Ljungdahl pathway in the early 1980’s, significant effort has been put into trying to characterize the substrate binding activity of CODH/ACS with the ''M. thermoacetica'' protein used as the model in most case studies <ref name="CN">PMID:19583207</ref>.  However, little progress was made in defining the exact structure of the protein with crystal structures until the 2000’s.  Several reasons why CODH/ACS has received so much attention include the fact that it contains highly disputed metalloclusters, its use of biological organometallic intermediates in reactions, and its contribution to reducing environmental pollutants <ref>PMID: 11841199</ref> <ref>PMID: 11848835</ref>.
+Similar bacteria which harbor monofunctional CODH enzymes include the autotrophs ''Rhodosprillum rubrum'' and ''Carboxydothermus  hydrogenoformans'' <ref name="Cu">PMID:12386327</ref>.  In addition, a variation on CODH/ACS termed CODH-containing acetyl-CoA decarboxylase/synthase is found in methanogenic  archea and decomposes acetyl-CoA to carbon dioxide and methane <ref>PMID: 18621675</ref>.
+PDB codes for the ''M. thermoacetica'' CODH/ACS enzyme are: 1MJG <ref>1MJG. [http://dx.doi.org/10.2210/pdb1mjg/pdb DOI:10.2210/pdb1mjg/pdb]</ref>  <scene name='Sandbox_Reserved_496/Codh_acs/1'>(orginial scene)</scene>, 1OAO <ref>1OAO. [http://dx.doi.org/10.2210/pdb1oao/pdb DOI:10.2210/pdb1oao/pdb]</ref>, 2Z8Y <ref>2Z8Y. [http://dx.doi.org/10.2210/pdb2z8y/pdb DOI:10.2210/pdb2z8y/pdb]</ref>, 3I01 <ref>3I01. [http://dx.doi.org/10.2210/pdb3i01/pdb DOI:10.2210/pdb3i01/pdb]</ref>, and 3I04 <ref>3I04. [http://dx.doi.org/10.2210/pdb3i04/pdb DOI:10.2210/pdb3i04/pdb]</ref>.
+==='''Structure'''===
+----
+The CODH/ACS enzyme from ''M. thermoacetica'' is an <scene name='Sandbox_Reserved_496/Codh_acs_tetramer/2'>α2β2 tetramer</scene> with seven metalloclusters. Each 674 residue <scene name='Sandbox_Reserved_496/Beta_subunits/2'>β subunit </scene>  carries out CODH activity, while each 729 residue <scene name='Sandbox_Reserved_496/Alpha_subunits/1'>α subunit</scene> is responsible for ACS activity.  From the N-terminus to C-terminus, <scene name='Sandbox_Reserved_496/Beta_secondary/1'> β subunit domains</scene> are as follows: an α-helical domain (residues 1-257) followed by two α/β Rossmann-like domains (residues 262-458 and 463-674). The β subunit has 57% helical and 9% β-sheet character with 31 helices and 15 β-strands. The  <scene name='Sandbox_Reserved_496/Alpha_secondary/1'>α subunit is also comprised of three domains</scene>, two with α+β folds and a third with a helical region (residues 1-154) at the N-terminus of a Rossmann (six-stranded α/β) fold (residues 155-316) which is similar to a portion of the β subunit structure <ref name="Cu"/> <ref name="Xe">PMID:18293927</ref>.  Overall, the α subunit has 50% helical and 14% β-sheet character with 36 helices and 22 β-strands.
+<scene name='Sandbox_Reserved_496/Beta_metalloclusters/1'>Five of the metalloclusters</scene> (<font color='red'>'''two B-'''</font>, <font color='blue'>'''two C-'''</font>, and <font color='green'>'''one D-cluster'''</font>) are located in the β<sub>2</sub> portion of the protein with a B- and C-cluster in each β subunit and the sole D-cluster bridging the two subunits.  The B- and D-clusters consist of [Fe<sub>4</sub>S<sub>4</sub>] centers that serve to transfer electrons.  As the active site in each β subunit where CODH activity occurs, the <scene name='Sandbox_Reserved_496/Beta_c_cluster/2'>C-clusters are composed of a Fe-[NiFe3S4] cage </scene> with the unique Fe coordinated by a bridging sulfur ion, His283, and Cys317 <ref name="Zn">PMID:12627225</ref>.  The B- and D-clusters are positioned in relation to the α-helical domain of the β subunit, while the C-clusters are aligned through interactions with both Rossmann-like domains <ref name="Xe"/>.  A ligand binding study with the native CODH/ACS structure and with cyanide used as competitive inhibitor for CO showed that H<sub>2</sub>O/OH<sup>-</sup> binds the C-cluster at the unique Fe and CO binds the C-cluster at the Ni ion <ref name="CN"/>.
+The remaining two metalloclusters (both A-clusters) are located in the two α subunits of the CODH/ACS protein.  As the active site of ACS activity in each α subunit, the A-clusters are composed of a [Fe<sub>4</sub>S<sub>4</sub>] center bridged to a binuclear site.  There is some debate regarding the metal ions present in the binuclear site; either <scene name='Sandbox_Reserved_496/Alpha_a_cluster/1'>both A-clusters are [Fe4S4]-Cu-Ni</scene> <ref name="Cu"/> or one A-cluster is <scene name='Sandbox_Reserved_496/A_cluster_ni_ni/1'>[Fe4S4]-Ni-Ni</scene>  while the other is <scene name='Sandbox_Reserved_496/A_cluster_zn_ni/1'>[Fe4S4]-Zn-Ni</scene>  <ref name="Zn"/>.  The [Fe<sub>4</sub>S<sub>4</sub>] center is coordinated by Cys506, Cys509, Cys518, and Cys528 with Cys509 also forming the bridge between the [Fe<sub>4</sub>S<sub>4</sub>] and the [http://en.wikipedia.org/wiki/Proximal#Proximal_and_distal proximal] metal ion.  Furthermore, the distal metal ion is coordinated by Cys595, Gly596, and Cys597 with Cys595 and Cys597 also connecting the distal and the proximal metal ions.  Only the [Fe<sub>4</sub>S<sub>4</sub>]-Ni-Ni  A-cluster is in an open conformation, the other two site types with Cu or Zn as the proximal ion are in closed form.
+Another characteristic feature of CODH/ACS is a 138Å long  <scene name='Sandbox_Reserved_496/Codh_acs_hydrophilic/1'>hydrophobic tunnel</scene> that connects the C- and A-clusters.  The cavity network formed by the hydrophobic tunnel is an S-shaped pore from C-cluster to C-cluster with two long branches that lead from the “S” to each A-cluster.  As the tunnel runs along nearly the full length of the protein, it enables the intramolecular diffusion of CO from the CODH active sites to the ACS active sites <ref name="Cu"/>.
+X-ray crystallography methods were used to determine the structure of CODH/ACS from ''M. thermoacetica''.  Crystals were formed by means of sitting drop vapor diffusion.  Both molecular replacement (using the CODH structure of ''R. rubrum'' <ref name="Cu"/> and ''C. hydrogenoformans'' <ref name="Zn"/>) and multiple-wavelength anomalous dispersion (MAD) methods were used to solve the structure’s diffraction pattern.  Resolution of the structures at the highest resolution shell ranges from 2.5Å to 1.9Å.
+==='''Mechanism of Action'''===
+----
+[[Image:A_cluster_1.JPG|frame|Proposed mechanism  1 for ACS activity with Cu-Ni ions in the binuclear site of the A-cluster. <ref name="Cu"/>]]
+'''β subunit reactions'''
+C-cluster (CODH activity): CO<sub>2</sub> + 2H<sup>+</sup> + 2e<sup>-</sup>  ↔  CO + H<sub>2</sub>O
+B- and D-clusters: electron transfer
+'''α subunit reactions'''
+A-cluster (ACS activity): CH<sub>3</sub>-Co(III)-CFeSP + CO + HSCoA  ↔  CH<sub>3</sub>-CO-SCoA +  Co(I)-CFeSP + H<sup>+</sup>
+There are two proposed mechanisms for the catalytic action of the A-cluster:  mechanism 1 uses Cu-Ni ions in the binuclear site while mechanism 2 uses Ni-Ni ions.
+Mechanism 1 suggests that CO created at the C-cluster travels through the hydrophobic tunnel and binds to Cu.  Next, the A-cluster switches to an open corrinoid conformation so that the methyl group may be transferred from the corrinoid iron-sulfur protein to the distal Ni ion of the active site.  The cluster reverts back to a solvent protected, closed form to generate the acetyl intermediate, and then reopens to allow HSCoA to bind.  HSCoA likely binds in the large cavity between the three domains of the α subunit where six Arg residues and Trp418 coincide.   Finally, HSCoA is deprotonated and acetylated to form acetyl-CoA <ref name="Cu"/>.
+{{clear}}
+[[Image:A_cluster_2.JPG|frame|Proposed mechanism  2 for ACS activity with Ni-Ni ions in the binuclear site of the A-cluster. <ref name="Zn"/>]]
-'''Cholix Toxin''' named also CT, is a protein toxin that uses ADP-ribosyltransferases to modify target proteins in human cells. The mono-ADP-ribosyltransferase toxins are bacterial virulence factors that are believed to be a factor in many disease states in animals plants as well even humans. For a list of various and other similar toxins see [[Toxins]].
+Mechanism 2 proposes that CO binds to the proximal Ni ion after exiting the tunnel.  The A-cluster then changes from the closed to the open conformation which closes the hydrophobic CO tunnel and provides a site for methyl group binding on the proximal Ni as it transitions from Ni(0) to Ni(II).  Next, the bound CO inserts into the Ni-CH<sub>3</sub> bond to produce an acetyl intermediate.  Lastly, deprotonated CoA-S<sup>-</sup> attacks the carbonyl carbon of the acetyl group to produce acetyl-CoA and the proximal Ni is reduced back to Ni(0) <ref name="Zn"/>.  Note that this mechanism differs from the former by binding both CO and CH<sub>3</sub> to the proximal metal ion and also the A-cluster stays open between methylation and CoA acetylation.
+{{clear}}
-<Structure load='569B' size='300' color='white' frame='true' align='right' caption='testcaption' />
+[[Image:C_cluster.JPG|frame|Proposed mechanism for CODH activity in the C-cluster. <ref name="CN"/>]]
+In the proposed catalytic action of the C-cluster, CO first binds the Ni ion followed by deprotonation of the Fe bound water to yield a reactive hydroxide which promotes nucleophilic attack of CO by the hydroxide.  Next, the Ni-COOH intermediate is deprotonated to Ni-COO<sup>-</sup> which allows release of CO<sub>2</sub> as the C-cluster is reduced to a new redox state.  Then, electrons are shuttled between the B- and D-clusters to reoxidize the C-cluster to its original redox state <ref name="CN"/>.   This catalytic cycle is of course operated in reverse to reduce CO<sub>2</sub> to CO and allow subsequent production of acetyl-CoA .
+{{clear}}
+==='''Possible Applications'''===
+----
+Since CODH/ACS consumes CO<sub>2</sub> it plays a direct part in the reduction of greenhouse gases by converting CO<sub>2</sub> into an intermediate which can transformed into more desirable products such as alcohols and acids.  A novel application in which CODH/ACS plays a role is the production of bioethanol from renewable natural resources such as wood, grasses, and agricultural residues (ex. corn stover).   In this process, the biomass undergoes [http://en.wikipedia.org/wiki/Gasification gasification] to yield CO, CO<sub>2</sub>, and H<sub>2</sub>.  The gases are subsequently fed to bacterial reactor systems containing organisms which utilize the Wood-Ljungdahl pathway and thus produce ethanol.   The main goal is to produce a renewable energy source that may be used as an alternative to petroleum.  However, at this time, the flux of carbon through the Wood-Ljungdahl pathway does not tend to favor ethanol production so much work remains to be done in this area.   On the other hand, the Wood-Ljungdahl pathway does produce significant levels of acetic acid, and to this extent, the pathway is considered a biological equivalent to the [http://en.wikipedia.org/wiki/Monsanto_process Monsanto process] for industrial acetic acid production <ref name="Berg"/>.  Roughly 10% of the total biological acetic acid production is attributable to anaerobic, autotrophic bacteria which possess CODH/ACS enzymes.
-== Cholix Toxin from ''Vibrio Cholerae ''==
+==='''References'''===
-The [http://en.wikipedia.org/wiki/Crystal_structure crystal structure] of the [http://en.wikipedia.org/wiki/Proteolysis proteolytically] activated monomeric form of Cyt2Ba was determined at 2.1Å resolution. It consists of a single domain of  <scene name='Cyt2Ba/Alpha_beta/5'>α/β</scene> architecture with a <scene name='Cyt2Ba/Beta/2'>β-sheet</scene> (yellow) surrounded by 2 <scene name='Cyt2Ba/Alpha/2'>α-helical</scene> layers <font color='red'><b>(red)</b></font> forming a cytolysin fold.
+----
+<references/>
+--[[User:Rachel Slivka|Rachel Slivka]]