Sandbox Reserved 496: Difference between revisions

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 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.       

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

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

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.

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 .

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.