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=== Oxidative ===
=== Oxidative ===


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.<ref name="pmid16895330">{{vcite2 journal | vauthors = Ragsdale SW | title = Metals and their scaffolds to promote difficult enzymatic reactions | journal = Chem. Rev. | volume = 106 | issue = 8 | pages = 3317–37 | date = August 2006 | pmid = 16895330 | doi = 10.1021/cr0503153 }}</ref> Based on IR spectra suggesting the presence of an Ni-CO complex, the proposed first step in the oxidative catalysis of CO to CO<sub>2</sub> involves the binding of CO to Ni<sup>2+</sup> and corresponding complexing of Fe<sup>2+</sup> to a water molecule.<ref>{{vcite2 journal | vauthors = Chen J, Huang S, Seravalli J, Gutzman H, Swartz DJ, Ragsdale SW, Bagley KA | title = Infrared Studies of Carbon Monoxide Binding to Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase from Moorella thermoacetica%u2020 | journal = Biochemistry | volume = 42 | issue = 50 | pages = 14822–14830 | year = 2003 | pmid = 14674756 | doi = 10.1021/bi0349470 }}</ref> The binding of CO molecule causes a shift in the coordination of the Ni atom from a square-planar to square pyramidal geometry.<ref>{{vcite2 journal | vauthors = Dobbek H, Svetlitchnyi V, Gremer L, Huber R, Meyer O | title = Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster | journal = Science | volume = 293 | issue = 5533 | pages = 1281 | year = 2001 | pmid = 11509720 | doi = 10.1126/science.1061500 | url = http://scienceonline.org/cgi/content/abstract/293/5533/1281 }}</ref> Dobbek et al. further propose that movement of the Nickel atom’s cysteine ligand brings the CO into close proximity to the hydroxyl group, and facilitate a base-catalyzed, nucleophillic attack by the iron-bound hydroxy group. A carboxy bridge between the Ni and Fe atom has been proposed as an intermediate.<ref>{{vcite2 journal | vauthors = Ha SW, Korbas M, Klepsch M, Meyer-Klaucke W, Meyer O, Svetlitchnyi V | title = Interaction of Potassium Cyanide with the [Ni-4Fe-5S] Active Site Cluster of CO Dehydrogenase from Carboxydothermus | journal = Journal of Biological Chemistry | volume = 14 | issue = 282 | pages = 10639–10646 | year = 2007 | pmid = 17277357 | doi = 10.1074/jbc.M610641200 | url = http://www.jbc.org/content/282/14/10639.abstract }}</ref> A decarboxylation leads to the release of CO<sub>2</sub> and the reduction of the cluster. Although the resulting intermediate oxidation state of the Ni and the degree to which electrons are distributed throughout the Ni-[3Fe-4S] cluster is subject of some debate, 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]].<ref name=Ragsdale>{{vcite2 journal | vauthors = Ragsdale SW | title = Nickel and the carbon cycle | journal = J Inorg Biochem. | volume = 101 | issue = Nov | pages = 1657–66 | pmid = 17716738 | pmc = 2100024 | doi = 10.1016/j.jinorgbio.2007.07.014 }}</ref>
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.<ref name="pmid16895330">{{vcite2 journal | vauthors = Ragsdale SW | title = Metals and their scaffolds to promote difficult enzymatic reactions | journal = Chem. Rev. | volume = 106 | issue = 8 | pages = 3317–37 | date = August 2006 | pmid = 16895330 | doi = 10.1021/cr0503153 }}</ref> Based on IR spectra suggesting the presence of an Ni-CO complex, the proposed first step in the oxidative catalysis of CO to CO<sub>2</sub> involves the binding of CO to Ni<sup>2+</sup> and corresponding complexing of Fe<sup>2+</sup> to a water molecule.<ref>{{vcite2 journal | vauthors = Chen J, Huang S, Seravalli J, Gutzman H, Swartz DJ, Ragsdale SW, Bagley KA | title = Infrared Studies of Carbon Monoxide Binding to Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase from Moorella thermoacetica%u2020 | journal = Biochemistry | volume = 42 | issue = 50 | pages = 14822–14830 | year = 2003 | pmid = 14674756 | doi = 10.1021/bi0349470 }}</ref> The binding of CO molecule causes a shift in the coordination of the Ni atom from a square-planar to square pyramidal geometry.<ref>{{vcite2 journal | vauthors = Dobbek H, Svetlitchnyi V, Gremer L, Huber R, Meyer O | title = Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster | journal = Science | volume = 293 | issue = 5533 | pages = 1281 | year = 2001 | pmid = 11509720 | doi = 10.1126/science.1061500 | url = http://scienceonline.org/cgi/content/abstract/293/5533/1281 }}</ref> Dobbek et al. further propose that movement of the Nickel atom’s cysteine ligand brings the CO into close proximity to the hydroxyl group, and facilitate a base-catalyzed, nucleophillic attack by the iron-bound hydroxy group. A carboxy bridge between the Ni and Fe atom has been proposed as an intermediate.<ref>{{vcite2 journal | vauthors = Ha SW, Korbas M, Klepsch M, Meyer-Klaucke W, Meyer O, Svetlitchnyi V | title = Interaction of Potassium Cyanide with the [Ni-4Fe-5S] Active Site Cluster of CO Dehydrogenase from Carboxydothermus | journal = Journal of Biological Chemistry | volume = 14 | issue = 282 | pages = 10639–10646 | year = 2007 | pmid = 17277357 | doi = 10.1074/jbc.M610641200 | url = http://www.jbc.org/content/282/14/10639.abstract }}</ref> A decarboxylation leads to the release of CO<sub>2</sub> and the reduction of the cluster. Although the resulting intermediate oxidation state of the Ni and the degree to which electrons are distributed throughout the Ni-[3Fe-4S] cluster is subject of some debate, 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]].<ref>
{{cite book
|first2=Stephen W.
|last2= Ragsdale
|first1=Vincent C.-C.
|last1= Wang
|first3=Fraser A.
|last3= Armstrong
|editor=Peter M.H. Kroneck and Martha E. Sosa Torres
|title=The Metal-Driven Biogeochemistry of Gaseous Compounds in the Environment
|series=Metal Ions in Life Sciences
|volume=14
|year=2014
|publisher=Springer
|chapter=Chapter 4. ''Investigations of the Efficient Electrocatalytic Interconversions of Carbon Dioxide and Carbon Monoxide by Nickel-Containing Carbon Monoxide Dehydrogenases''
|pages= 71-97
|doi=10.1007/978-94-017-9269-1_4
}}
</ref><ref name=Ragsdale>{{vcite2 journal | vauthors = Ragsdale SW | title = Nickel and the carbon cycle | journal = J Inorg Biochem. | volume = 101 | issue = Nov | pages = 1657–66 | pmid = 17716738 | pmc = 2100024 | doi = 10.1016/j.jinorgbio.2007.07.014 }}</ref>


=== Reductive ===
=== Reductive ===

Revision as of 09:43, 5 March 2015

carbon-monoxide dehydrogenase (acceptor)
Identifiers
EC no.1.2.99.2
CAS no.64972-88-9
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In enzymology, carbon monoxide dehydrogenase (EC 1.2.99.2) is an enzyme that catalyzes the chemical reaction

CO + H2O + A CO2 + AH2

The 3 substrates of this enzyme are CO, H2O, and A, whereas its two products are CO2 and AH2.

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.

Classes

Two major classes of the carbon monoxide dehydrogenase (CODH) enzymes have been identified. CODH containing a Mo-[2Fe-2S]-FAD active site have been found in aerobic bacteria, while a distinct class of Ni-[3Fe-4S] CODH enzymes have been purified from anaerobic bacteria.[1][2][3] Both classes of CODH catalyze the reversible conversion between carbon dioxide (CO2) and carbonmonoxide (CO). CODH exists in both monofuctional and bifunctional forms. In the latter case, CODH forms a bifunctional cluster with acetyl-CoA synthase, as has been well characterized in the anaerobic bacteria Moorella thermoacetica.[4][5]

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

Multiple research groups have proposed crystal structures for the α2β2 tetrameric enzyme CODH/ACS from the acetogenic bacteria M. thermoacetica, including two recent examples since 2009: 3I01 2Z8Y. The two β units are the site of CODH activity and form the central core of the enzyme. In total, the 310 kDa enzyme contains seven iron-sulfur [4Fe-4S] clusters. 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.[2][3]

A noteworthy feature of the M.thermoacetica CODH/ACS is an internal gas tunnel connecting the multiple active sites.[6] The full role of the gas channel in regulating the rate catalytic activity is still a subject of investigation, but several studies support the notion that molecules of CO do in fact travel directly from the C-cluster to the ACS active site without leaving the enzyme. For instance, the rate of acetyl-CoA synthase activity in the bifunctional enzyme is not affected by the addition of hemoglobin, which would compete for CO in bulk solution,[7] 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.[8] Protein engineering of the CODH/ACS in M.thermoacetica revealed that mutating residues, so as to functionally block the tunnel, stopped acety-CoA synthesis when only CO2 was present.[9] 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.[10]

Reaction mechanisms

Oxidative

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.[11] 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.[12] The binding of CO molecule causes a shift in the coordination of the Ni atom from a square-planar to square pyramidal geometry.[13] Dobbek et al. further propose that movement of the Nickel atom’s cysteine ligand brings the CO into close proximity to the hydroxyl group, and facilitate a base-catalyzed, nucleophillic attack by the iron-bound hydroxy group. A carboxy bridge between the Ni and Fe atom has been proposed as an intermediate.[14] A decarboxylation leads to the release of CO2 and the reduction of the cluster. Although the resulting intermediate oxidation state of the Ni and the degree to which electrons are distributed throughout the Ni-[3Fe-4S] cluster is subject of some debate, 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.[15][16]

Reductive

Given CODH's role in CO2 fixation identified in diverse autotrophic bacteria and archaea, it is common in the biochemistry literature for the reductive mechanism to be inferred as the “direct reverse” of the oxidative mechanism by the ”principal of microreversibility.”[17] In the process of reducing carbon dioxide, the enzyme's C-cluster must first be activated from an oxidized to a reduced state before the Ni-CO2 bond is formed.[18]

Function

Carbon monoxide dehydrogenase participates in diverse prokaryotic biochemical pathways, including the metabolism of methanogenic, aerobic carboxidotrophic, acetogenic bacteria, sulfate-reducing, and hydrogenogenic bacteria.[2] 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 rubram, 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.[19]

Environmental relevance

CODH is important for maintaining current atmospheric conditions. Microbial metabolism of CO maintains ambient CO at levels safe for other forms of life.[20]

References

  1. ^ Dobbek, Holger (2014). "Chapter 3. Carbon Monoxide. Toxic Gas and Fuel for Anaerobes and Aerobes: Carbon Monoxide Dehydrogenases". In Peter M.H. Kroneck and Martha E. Sosa Torres (ed.). The Metal-Driven Biogeochemistry of Gaseous Compounds in the Environment. Metal Ions in Life Sciences. Vol. 14. Springer. pp. 37–69. doi:10.1007/978-94-017-9269-1_3.
  2. ^ a b c 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): 1281–5. doi:10.1126/science.1061500. PMID 11509720.
  3. ^ a b Lindahl PA (2009). "Nickel-Carbon Bonds in Acetyl-Coenzyme A Synthases/Carbon Monoxide Dehydrogenases". In Sigel, Helmut; Sigel, Astrid (ed.). Metal-Carbon Bonds in Enzymes and Cofactors (Metal Ions in Life Sciences). Cambridge, Eng: Royal Society of Chemistry. doi:10.1039/9781847559333. ISBN 1-84755-915-8.{{cite book}}: CS1 maint: multiple names: editors list (link) Cite error: The named reference "isbn1-84755-915-8" was defined multiple times with different content (see the help page).
  4. ^ Doukov TI, Blasiak LC, Seravalli J, Ragsdale SW, Drennan CL (March 2008). "Xenon in and at the end of the tunnel of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase". Biochemistry. 47 (11): 3474–83. doi:10.1021/bi702386t. PMC 3040099. PMID 18293927.
  5. ^ Tan X, Volbeda A, Fontecilla-Camps JC, Lindahl PA (April 2006). "Function of the tunnel in acetylcoenzyme A synthase/carbon monoxide dehydrogenase". J. Biol. Inorg. Chem. 11 (3): 371–8. doi:10.1007/s00775-006-0086-9. PMID 16502006.
  6. ^ Doukov TI, Blasiak LC, Seravalli J, Ragsdale SW, Drennan CL (March 2008). "Xenon in and at the end of the tunnel of bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase". Biochemistry. 47 (11): 3474–83. doi:10.1021/bi702386t. PMC 3040099. PMID 18293927.
  7. ^ Doukov TI, Iverson TM, Seravalli J, Ragsdale SW, Drennan CL (2002). "A Ni-Fe-Cu center in a bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase" (PDF). Science. 298 (5593): 567. doi:10.1126/science.1075843. PMID 12386327.
  8. ^ Seravalli J, Ragsdale SW (2000). "Channeling of Carbon Monoxide during Anaerobic Carbon Dioxide Fixation". Biochemistry. 39 (6): 1274–1277. doi:10.1021/bi991812e. PMID 10684606.
  9. ^ Tan X, Loke HK, Fitch S, Lindahl PA (2005). "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. doi:10.1021/ja043701v. PMID 15839681.
  10. ^ Weeks A, Lund L, Raushel FM (2006). "Tunneling of intermediates in enzyme-catalyzed reactions". Current Opinion in Chemical Biology. 10 (5): 465–472. doi:10.1016/j.cbpa.2006.08.008. PMID 16931112.
  11. ^ Ragsdale SW (August 2006). "Metals and their scaffolds to promote difficult enzymatic reactions". Chem. Rev. 106 (8): 3317–37. doi:10.1021/cr0503153. PMID 16895330.
  12. ^ Chen J, Huang S, Seravalli J, Gutzman H, Swartz DJ, Ragsdale SW, Bagley KA (2003). "Infrared Studies of Carbon Monoxide Binding to Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase from Moorella thermoacetica%u2020". Biochemistry. 42 (50): 14822–14830. doi:10.1021/bi0349470. PMID 14674756.
  13. ^ Dobbek H, Svetlitchnyi V, Gremer L, Huber R, Meyer O (2001). "Crystal structure of a carbon monoxide dehydrogenase reveals a [Ni-4Fe-5S] cluster". Science. 293 (5533): 1281. doi:10.1126/science.1061500. PMID 11509720.
  14. ^ Ha SW, Korbas M, Klepsch M, Meyer-Klaucke W, Meyer O, Svetlitchnyi V (2007). "Interaction of Potassium Cyanide with the [Ni-4Fe-5S] Active Site Cluster of CO Dehydrogenase from Carboxydothermus". Journal of Biological Chemistry. 14 (282): 10639–10646. doi:10.1074/jbc.M610641200. PMID 17277357.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  15. ^ Wang, Vincent C.-C.; Ragsdale, Stephen W.; Armstrong, Fraser A. (2014). "Chapter 4. Investigations of the Efficient Electrocatalytic Interconversions of Carbon Dioxide and Carbon Monoxide by Nickel-Containing Carbon Monoxide Dehydrogenases". In Peter M.H. Kroneck and Martha E. Sosa Torres (ed.). The Metal-Driven Biogeochemistry of Gaseous Compounds in the Environment. Metal Ions in Life Sciences. Vol. 14. Springer. pp. 71–97. doi:10.1007/978-94-017-9269-1_4.
  16. ^ Ragsdale SW. "Nickel and the carbon cycle". J Inorg Biochem. 101 (Nov): 1657–66. doi:10.1016/j.jinorgbio.2007.07.014. PMC 2100024. PMID 17716738.
  17. ^ Ragsdale SW, Pierce E (December 2008). "Acetogenesis and the Wood-Ljungdahl pathway of CO(2) fixation". Biochim. Biophys. Acta. 1784 (12): 1873–98. doi:10.1016/j.bbapap.2008.08.012. PMC 2646786. PMID 18801467.
  18. ^ Feng J, Lindahl PA (February 2004). "Carbon monoxide dehydrogenase from Rhodospirillum rubrum: effect of redox potential on catalysis". Biochemistry. 43 (6): 1552–9. doi:10.1021/bi0357199. PMID 14769031.
  19. ^ Hegg EL (October 2004). "Unraveling the structure and mechanism of acetyl-coenzyme A synthase". Acc. Chem. Res. 37 (10): 775–83. doi:10.1021/ar040002e. PMID 15491124.
  20. ^ Bartholomew, G.W.; Alexander, M. (1979). "Microbial metabolism of carbon monoxide in culture and in soil". Applied and Environmental Microbiology. 37 (5): 932. Retrieved 2010-05-15.

Further reading

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