Sandbox Reserved 496: Difference between revisions

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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>.  

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> (shown at right), 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>.

The CODH/ACS enzyme from ''M. thermoacetica'' is an α2β2 tetramer with seven metalloclusters. Each 674 residue <scene name='Sandbox_Reserved_496/Beta_subunits/1'>β subunit</scene>  β subunit carries out CODH activity, while each 729 residue α subunit is responsible for ACS activity.  From the N- terminus to C-terminus, the domains of the β subunit 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 α subunit is also comprised of three domains, 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.

 

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 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.