Biology:Carbon monoxide dehydrogenase

From HandWiki
Short description: Class of enzymes
carbon-monoxide dehydrogenase (acceptor)
Identifiers
EC number1.2.7.4
CAS number64972-88-9
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO

In enzymology, carbon monoxide dehydrogenase (CODH) (EC 1.2.7.4) is an enzyme that catalyzes the chemical reaction

CO + H2O + A [math]\displaystyle{ \rightleftharpoons }[/math] CO2 + AH2

The chemical process catalyzed by carbon monoxide dehydrogenase is similar to the water-gas shift reaction.

The 3 substrates of this enzyme are CO, H2O, and A, whereas its two products are CO2 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 Ferredoxin, NADP+/NADPH and flavoprotein complexes like flavin adenine dinucleotide (FAD) as well as hydrogenases.[1][2][3][4] CODHs support the metabolisms of diverse prokaryotes, including methanogens, aerobic carboxidotrophs, acetogens, sulfate-reducers, and hydrogenogenic bacteria. The bidirectional reaction catalyzed by CODH plays a role in the carbon cycle allowing organisms to both make use of CO as a source of energy and utilize CO2 as a source of carbon. CODH can form a monofunctional enzyme, as is the case in Rhodospirillum rubrum, or can form a cluster with acetyl-CoA synthase as has been shown in M. thermoacetica. When acting in concert, either as structurally independent enzymes or in a bifunctional CODH/ACS unit, the two catalytic sites are key to carbon fixation in the reductive acetyl-CoA pathway. Microbial organisms (Both aerobic and anaerobic) encode and synthesize CODH for the purpose of carbon fixation (CO oxidation and CO2 reduction). Depending on attached accessory proteins (A,B,C,D-Clusters), serve a variety of catalytic functions, including reduction of [4Fe-4S] clusters and insertion of nickel.[5]

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.[6][7][8] Both classes of CODH catalyze the conversion of carbon monoxide (CO) to carbon dioxide (CO2). Only the Ni containing CODH is able to also catalyze the back reaction. CODHs exist in both monofunctional and bifunctional forms. An example for the latter case, Ni,Fe-CODHs form a bifunctional cluster with acetyl-CoA synthase, as has been well characterized in the anaerobic bacteria Moorella thermoacetica,[9][10] Clostridium autoethanogenum [11] and Carboxydothermus hydrogenoformans [12]. While the ACS subunits of the complex of C. autoethanogenum show a rather extended arrangement [11] those of the M. thermoacetica and C. hydrogenoformans complex are closer to the CODH subunits forming a tight tunnel network connecting cluster C and cluster A.[13][12]

Ni,Fe-CODH

Nickel containing CODH (Ni,Fe-CODH) can be further divided into structural clades, dependent on their phylogenetic relationship[14]

Structure

Structure of CODH/ACS in M.thermoacetica." Alpha (ACS) and beta (CODH) subunits are shown. (1)The A-cluster Ni-[4Fe-4S]. (2)C-cluster Ni-[3Fe-4S]. (3) B-Cluster [4Fe-4S]. (4) D-cluster [4Fe-4S]. Designed from 3I01

Ni,Fe-CODH

Homodimeric Ni,Fe-CODHs contain five-metal clusters.[15] They exist either in a homodimeric form (also called monofunctional) or in a bifunctional α2β2-tetrameric complex with acetyl-CoA synthase (ACS).

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 Acetogens undergo the Wood-Ljungdahl Pathway, relying on CODH to produce CO by reduction of CO2 needed for the synthesis of Acetyl-CoA from a methyl, coenzyme a (CoA) and corrinoid iron-sulfur protein.[29] Other types show CODH being utilized to generate a proton motive force for the purposes of energy generation. CODH is used for the CO oxidation, producing two protons which are subsequently reduced to form dihydrogen (H2.[30]

References

  1. ↑ "Flavin-Based Electron Bifurcation, Ferredoxin, Flavodoxin, and Anaerobic Respiration With Protons (Ech) or NAD+ (Rnf) as Electron Acceptors: A Historical Review". Frontiers in Microbiology 9: 401. 2018. doi:10.3389/fmicb.2018.00401. PMID 29593673. 
  2. ↑ "Redox dependent metabolic shift in Clostridium autoethanogenum by extracellular electron supply". Biotechnology for Biofuels 9 (1): 249. December 2016. doi:10.1186/s13068-016-0663-2. PMID 27882076. 
  3. ↑ "The hybrid-cluster protein ('prismane protein') from Escherichia coli. Characterization of the hybrid-cluster protein, redox properties of the [2Fe-2S] and [4Fe-2S-2O] clusters and identification of an associated NADH oxidoreductase containing FAD and [2Fe-2S]". European Journal of Biochemistry 267 (3): 666–676. February 2000. doi:10.1046/j.1432-1327.2000.01032.x. PMID 10651802. 
  4. ↑ "Biome-specific distribution of Ni-containing carbon monoxide dehydrogenases". Extremophiles 26 (1): 9. January 2022. doi:10.1007/s00792-022-01259-y. PMID 35059858. 
  5. ↑ "The Carbon Monoxide Dehydrogenase from Desulfovibrio vulgaris". Biochimica et Biophysica Acta (BBA) - Bioenergetics 1847 (12): 1574–1583. December 2015. doi:10.1016/j.bbabio.2015.08.002. PMID 26255854. 
  6. ↑ "Chapter 3. Carbon Monoxide. Toxic Gas and Fuel for Anaerobes and Aerobes: Carbon Monoxide Dehydrogenases". The Metal-Driven Biogeochemistry of Gaseous Compounds in the Environment. Metal Ions in Life Sciences. 14. Springer. 2014. pp. 37–69. doi:10.1007/978-94-017-9269-1_3. 
  7. ↑ 7.0 7.1 7.2 7.3 7.4 "Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster". Science 293 (5533): 1281–1285. August 2001. doi:10.1126/science.1061500. PMID 11509720. Bibcode: 2001Sci...293.1281D. 
  8. ↑ 8.0 8.1 Metal-Carbon Bonds in Enzymes and Cofactors. Metal Ions in Life Sciences. Royal Society of Chemistry. September 2010. doi:10.1039/9781847559333. ISBN 978-1-84755-915-9. 
  9. ↑ 9.0 9.1 9.2 "Xenon in and at the end of the tunnel of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase". Biochemistry 47 (11): 3474–3483. March 2008. doi:10.1021/bi702386t. PMID 18293927. 
  10. ↑ 10.0 10.1 "Function of the tunnel in acetylcoenzyme A synthase/carbon monoxide dehydrogenase". Journal of Biological Inorganic Chemistry 11 (3): 371–378. April 2006. doi:10.1007/s00775-006-0086-9. PMID 16502006. 
  11. ↑ 11.0 11.1 11.2 11.3 "Gas channel rerouting in a primordial enzyme: Structural insights of the carbon-monoxide dehydrogenase/acetyl-CoA synthase complex from the acetogen Clostridium autoethanogenum". Biochimica et Biophysica Acta (BBA) - Bioenergetics 1862 (1): 148330. January 2021. doi:10.1016/j.bbabio.2020.148330. PMID 33080205. 
  12. ↑ 12.0 12.1 12.2 12.3 "On the Kinetics of CO 2 Reduction by Ni, Fe-CO Dehydrogenases" (in en). ACS Catalysis 12 (20): 13131–13142. 2022-10-21. doi:10.1021/acscatal.2c02221. ISSN 2155-5435. 
  13. ↑ 13.0 13.1 "A Ni-Fe-Cu center in a bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase". Science 298 (5593): 567–572. October 2002. doi:10.1126/science.1075843. PMID 12386327. Bibcode: 2002Sci...298..567D. [yes|permanent dead link|dead link}}]
  14. ↑ "Structural and Phylogenetic Diversity of Anaerobic Carbon-Monoxide Dehydrogenases". Frontiers in Microbiology 9: 3353. 2019-01-17. doi:10.3389/fmicb.2018.03353. PMID 30705673. 
  15. ↑ 15.0 15.1 "Redox-dependent rearrangements of the NiFeS cluster of carbon monoxide dehydrogenase". eLife 7: e39451. October 2018. doi:10.7554/eLife.39451. PMID 30277213. 
  16. ↑ "Nickel is required for the transfer of electrons from carbon monoxide to the iron-sulfur center(s) of carbon monoxide dehydrogenase from Rhodospirillum rubrum". Biochemistry 28 (12): 4968–4973. June 1989. doi:10.1021/bi00438a010. PMID 2504284. 
  17. ↑ 17.0 17.1 "Life on carbon monoxide: X-ray structure of Rhodospirillum rubrum Ni-Fe-S carbon monoxide dehydrogenase". Proceedings of the National Academy of Sciences of the United States of America 98 (21): 11973–11978. October 2001. doi:10.1073/pnas.211429998. PMID 11593006. Bibcode: 2001PNAS...9811973D. 
  18. ↑ "Structural basis of cyanide inhibition of Ni, Fe-containing carbon monoxide dehydrogenase". Journal of the American Chemical Society 131 (29): 9922–9923. July 2009. doi:10.1021/ja9046476. PMID 19583208. 
  19. ↑ "Carbon dioxide activation at the Ni,Fe-cluster of anaerobic carbon monoxide dehydrogenase". Science 318 (5855): 1461–1464. November 2007. doi:10.1126/science.1148481. PMID 18048691. Bibcode: 2007Sci...318.1461J. 
  20. ↑ "Channeling of carbon monoxide during anaerobic carbon dioxide fixation". Biochemistry 39 (6): 1274–1277. February 2000. doi:10.1021/bi991812e. PMID 10684606. 
  21. ↑ "The tunnel of acetyl-coenzyme a synthase/carbon monoxide dehydrogenase regulates delivery of CO to the active site". Journal of the American Chemical Society 127 (16): 5833–5839. April 2005. doi:10.1021/ja043701v. PMID 15839681. 
  22. ↑ "Tunneling of intermediates in enzyme-catalyzed reactions". Current Opinion in Chemical Biology 10 (5): 465–472. October 2006. doi:10.1016/j.cbpa.2006.08.008. PMID 16931112. 
  23. ↑ "Metals and their scaffolds to promote difficult enzymatic reactions". Chemical Reviews 106 (8): 3317–3337. August 2006. doi:10.1021/cr0503153. PMID 16895330. 
  24. ↑ "Substrate Activation at the Ni,Fe Cluster of CO Dehydrogenases: The Influence of the Protein Matrix" (in en). ACS Catalysis 12 (20): 12711–12719. 2022-10-21. doi:10.1021/acscatal.2c02922. ISSN 2155-5435. 
  25. ↑ "Infrared studies of carbon monoxide binding to carbon monoxide dehydrogenase/acetyl-CoA synthase from Moorella thermoacetica". Biochemistry 42 (50): 14822–14830. December 2003. doi:10.1021/bi0349470. PMID 14674756. 
  26. ↑ "Interaction of potassium cyanide with the [Ni-4Fe-5S] active site cluster of CO dehydrogenase from Carboxydothermus hydrogenoformans". The Journal of Biological Chemistry 282 (14): 10639–10646. April 2007. doi:10.1074/jbc.M610641200. PMID 17277357. 
  27. ↑ Peter M.H. Kroneck, ed (2014). "Investigations of the Efficient Electrocatalytic Interconversions of Carbon Dioxide and Carbon Monoxide by Nickel-Containing Carbon Monoxide Dehydrogenases". The Metal-Driven Biogeochemistry of Gaseous Compounds in the Environment. Metal Ions in Life Sciences. 14. Springer. pp. 71–97. doi:10.1007/978-94-017-9269-1_4. ISBN 978-94-017-9268-4. 
  28. ↑ "Nickel and the carbon cycle". Journal of Inorganic Biochemistry 101 (11–12): 1657–1666. November 2007. doi:10.1016/j.jinorgbio.2007.07.014. PMID 17716738. 
  29. ↑ 29.0 29.1 "Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation". Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1784 (12): 1873–1898. December 2008. doi:10.1016/j.bbapap.2008.08.012. PMID 18801467. 
  30. ↑ "Characterization of the CO oxidation/H2 evolution system of Rhodospirillum rubrum. Role of a 22-kDa iron-sulfur protein in mediating electron transfer between carbon monoxide dehydrogenase and hydrogenase". The Journal of Biological Chemistry 266 (27): 18395–18403. September 1991. doi:10.1016/S0021-9258(18)55283-2. PMID 1917963. 

Further reading



Retrieved from "https://handwiki.org/wiki/index.php?title=Biology:Carbon_monoxide_dehydrogenase&oldid=3679391"