Carbon monoxide dehydrogenase
carbon-monoxide dehydrogenase (acceptor) | |||||||||
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Identifiers | |||||||||
ExPASy | NiceZyme view | ||||||||
KEGG | KEGG entry | ||||||||
MetaCyc | metabolic pathway | ||||||||
PRIAM | profile | ||||||||
PDB structures | RCSB PDB PDBe PDBsum | ||||||||
Gene Ontology | AmiGO / QuickGO | ||||||||
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In
- CO + H2O + A CO2 + AH2
The chemical process catalyzed by carbon monoxide dehydrogenase is similar to the
The 3
and AH2.A variety of electron donors/receivers (Shown as "A" and "AH2" in the reaction equation above) are observed in micro-organisms which utilize CODH. Several examples of electron transfer cofactors have been proposed, including
This enzyme belongs to the family of oxidoreductases, specifically those acting on the aldehyde or oxo group of donor with other acceptors. The systematic name of this enzyme class is carbon-monoxide:acceptor oxidoreductase. Other names in common use include anaerobic carbon monoxide dehydrogenase, carbon monoxide oxygenase, carbon-monoxide dehydrogenase, and carbon-monoxide:(acceptor) oxidoreductase.
Diversity
CODH are a rather diverse group of enzymes, containing two unrelated types of CODH. A copper-molybdenum flavoenzymes is found in some aerobic carboxydotrophic bacteria. Anaerobic bacteria utilize nickel-iron based CODHs.
Ni,Fe-CODH
Nickel containing CODH (Ni,Fe-CODH) can be further divided into structural clades, dependent on their phylogenetic relationship[14]
Structure
Ni,Fe-CODH
Monofunctional
The best studied monofunctional CODHs are those of Desulfovibrio vulgaris,[15] Rhodospirillum rubrum [16][17] and Carboxydothermus hydrogenoformans. [18][19][7] They are homodimers of around 130 kDa sharing a central [4Fe4S]-cluster at the surface of the protein - cluster D. The electrons are probably transferred to another [4Fe4S]-cluster (cluster B) located 10 A inside the protein and from there to the active site - cluster C, being an [Ni4Fe4S]-cluster. [7] [17]
Bifunctional
The CODH/ACS complex is an α2β2 tetrameric enzyme. The structures of CODH/ACS complexes of the anaerobic bacteria Moorella thermoacetica,[9][10] Clostridium autoethanogenum [11] and Carboxydothermus hydrogenoformans [12] have been solved. The two CODH subunits form the central core of the enzyme to which an ACS subunit is attached at each side. Each α unit contains a single metal cluster. Together, the two β units contains five clusters of three types. CODH catalytic activity occurs at the Ni-[3Fe-4S] C-clusters while the interior [4Fe-4S] B and D clusters transfer electrons away from the C-cluster to external electron carriers such as ferredoxin. The ACS activity occurs in A-cluster located in the outer two α units.[7][8]
All CODH/ACS complexes have a gas tunnel connecting the multiple active sites, while the tunnel system in the C. autoethanogenum enzyme is comparatively open and those of M. thermoacetica and C. hydrogenoformans rather tight.[9][11][12] For the Moorella enzyme the rate of acetyl-CoA synthase activity from CO2 is not affected by the addition of hemoglobin, which would compete for CO in bulk solution,[13] and isotopic labeling studies show that carbon monoxide derived from the C-cluster is preferentially used at the A-cluster over unlabeled CO in solution.[20] Protein engineering of the CODH/ACS in M.thermoacetica revealed that mutating residues, so as to functionally block the tunnel, stopped acetyl-CoA synthesis when only CO2 was present.[21] The discovery of a functional CO tunnel places CODH on a growing list of enzymes that independently evolved this strategy to transfer reactive intermediates from one active site to another.[22]
Reaction mechanisms
Ni,Fe-CODH
The CODH catalytic site, referred to as the C-cluster, is a [3Fe-4S] cluster bonded to a Ni-Fe moiety. Two basic amino acids (Lys587 and His 113 in M.thermoacetica) reside in proximity to the C-cluster and facilitate acid-base chemistry required for enzyme activity.[23] Furthermore, other residues (i.e. an isoleucine apical to the Ni atom) fine-tune the binding and conversion of CO.[24] Based on IR spectra suggesting the presence of an Ni-CO complex, the proposed first step in the oxidative catalysis of CO to CO2 involves the binding of CO to Ni2+ and corresponding complexing of Fe2+ to a water molecule.[25]
It has been proposed that CO binds to square-planar nickel where it converts to a carboxy bridge between the Ni and Fe atom.[7][26] A decarboxylation leads to the release of CO2 and the reduction of the cluster.
The electrons in the reduced C-cluster are transferred to nearby B and D [4Fe-4S] clusters, returning the Ni-[3Fe-4S] C-cluster to an oxidized state and reducing the single electron carrier ferredoxin.[27][28]
Given CODH's role in CO2 fixation, the reductive mechanism is sometimes inferred as the “direct reverse” of the oxidative mechanism by the ”principle of microreversibility.”[29]
Environmental relevance
Carbon monoxide dehydrogenase regulates atmospheric CO and CO2 levels. Anaerobic micro-organisms like
References
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Further reading
- Jeoung JH, Martins BM, Dobbek H (2019). "Carbon Monoxide Dehydrogenases". In Hu Y (ed.). Metalloproteins. Methods in Molecular Biology. Vol. 1876. New York: Springer. pp. 37–54. S2CID 52980499.
- Jeoung JH, Dobbek H (November 2007). "Carbon dioxide activation at the Ni,Fe-cluster of anaerobic carbon monoxide dehydrogenase". Science. 318 (5855). American Association for the Advancement of Science: 1461–1464. S2CID 41063549.
- Dobbek H, Svetlitchnyi V, Gremer L, Huber R, Meyer O (August 2001). "Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster". Science. 293 (5533): 1281–1285. S2CID 29401674.
- Hu Z, Spangler NJ, Anderson ME, Xia J, Ludden PW, Lindahl PA, Münck E (January 1996). "Nature of the C-Cluster in Ni-Containing Carbon Monoxide Dehydrogenases". Journal of the American Chemical Society. 118 (4): 830–845. ISSN 0002-7863.
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