View source for CO-methylating acetyl-CoA synthase

{{Short description|Enzyme}}
{{infobox enzyme
| Name       = CO-methylating acetyl-CoA synthase
| EC_number  = 2.3.1.169
| CAS_number =
| GO_code    = 0043884
| image      = PDB_1ru3_EBI.jpg
| width      = 
| caption    = Monomeric Acetyl-CoA synthase 
}}

'''Acetyl-CoA synthase''' (ACS), not to be confused with [[acetyl-CoA synthetase]] or acetate-CoA ligase (ADP forming), is a [[nickel]]-containing enzyme involved in the metabolic processes of cells. Together with [[carbon monoxide dehydrogenase]] (CODH), it forms the bifunctional enzyme Acetyl-CoA Synthase/Carbon Monoxide Dehydrogenase (ACS/CODH) found in [[Anaerobic organism|anaerobic microorganisms]] such as [[archaea]] and [[bacteria]].<ref name="Lindahl_2004">{{cite journal | vauthors = Lindahl PA | title = Acetyl-coenzyme A synthase: the case for a Ni(p)(0)-based mechanism of catalysis | journal = Journal of Biological Inorganic Chemistry | volume = 9 | issue = 5 | pages = 516–24 | date = July 2004 | pmid = 15221478 | doi = 10.1007/s00775-004-0564-x | s2cid = 21597571 }}</ref> The ACS/CODH enzyme works primarily through the [[Wood–Ljungdahl pathway]] which converts [[carbon dioxide]] to [[Acetyl-CoA]]. The recommended name for this enzyme is '''CO-methylating acetyl-CoA synthase'''.<ref name="Handbook of enzymes">{{cite book|title=Springer handbook of enzymes|volume=30|pages=459–466}}</ref>

==Chemistry==

In nature, there are six different pathways where CO{{sub|2}} is fixed. Of these, the [[Wood–Ljungdahl pathway]] is the predominant sink in anaerobic conditions. Acetyl-CoA Synthase (ACS) and [[carbon monoxide dehydrogenase]] (CODH) are integral enzymes in this one pathway and can perform diverse reactions in the [[carbon cycle]] as a result. Because of this, the exact activity of these molecules has come under intense scrutiny over the past decade.<ref name="Can, Armstrong Ragsdale review">{{cite journal | vauthors = Can M, Armstrong FA, Ragsdale SW | title = Structure, function, and mechanism of the nickel metalloenzymes, CO dehydrogenase, and acetyl-CoA synthase | journal = Chemical Reviews | volume = 114 | issue = 8 | pages = 4149–74 | date = April 2014 | pmid = 24521136 | pmc = 4002135 | doi = 10.1021/cr400461p }}</ref>

===Wood–Ljungdahl pathway===

The [[Wood–Ljungdahl pathway]] consists of two different reactions that break down carbon dioxide. The first pathway involves CODH converting [[carbon dioxide]] into [[carbon monoxide]] through a two-electron transfer, and the second reaction involves ACS synthesizing [[acetyl-CoA]] using the [[carbon monoxide]] from CODH together with coenzyme-A (CoA) and a methyl group from a [[corrinoid iron-sulfur protein]], CFeSP.<ref name="Hegg mechanism ACS">{{cite journal | vauthors = Hegg EL | title = Unraveling the structure and mechanism of acetyl-coenzyme A synthase | journal = Accounts of Chemical Research | volume = 37 | issue = 10 | pages = 775–83 | date = October 2004 | pmid = 15491124 | doi = 10.1021/ar040002e }}</ref> The two main overall reactions are as follows:

{{NumBlk|:|<chem>CO2 + 2H+ + 2e- <=> CO + H2O</chem>|{{EquationRef|1}}}}
{{NumBlk|:|<math chem>\ce{CO + CH3-CFeSP + CoA <=>} \text{ acetyl-CoA} + \ce{CFeSP}</math>|{{EquationRef|2}}}}
The [[acetyl-CoA]] produced can be used in a variety of ways depending on the needs of the organism. For example, [[Acetogenesis|acetate-forming bacteria]] use [[acetyl-CoA]] for their [[autotroph]]ic growth processes, and [[Methanogenesis|methanogenic]] archae such as ''Methanocarcina barkeri'' convert the acetyl-CoA into acetate and use it as an alternative source of carbon instead of CO{{sub|2}}.<ref name="Riordan review">{{cite journal | vauthors = Riordan CG | title = Synthetic chemistry and chemical precedents for understanding the structure and function of acetyl coenzyme A synthase | journal = Journal of Biological Inorganic Chemistry | volume = 9 | issue = 5 | pages = 542–9 | date = July 2004 | pmid = 15221481 | doi = 10.1007/s00775-004-0567-7 | s2cid = 6536992 }}</ref>

[[File:ACS Autotrophic growth and acetate synthesis.jpg|thumb|[[Auxotrophy|Autotrophic]] growth via the Wood–Ljungdahl pathway. Adapted from Ragsdale et al.<ref name="Can, Armstrong Ragsdale review" />]]

[[Acetogenic]] bacteria use this method to generate acetate and [[acetic acid]]. Since the above two reactions are reversible, it opens up a diverse range of reactions in the carbon cycle. In addition to acetyl-CoA production, the reverse can occur with ACS producing CO and returning the methyl piece back to the corrinoid protein.

Along with the process of [[methanogenesis]], organisms can subsequently convert the acetate to methane. Furthermore, the Wood-Ljungdahl pathway allows for the anaerobic oxidation of acetate where [[Adenosine triphosphate|ATP]] is used to convert acetate into acetyl-CoA, which is then broken down by ACS to produce carbon dioxide that is released into the atmosphere.<ref name="Ragsdale Chem Rev 1996">{{cite journal|last1=Ragsdale|first1=Stephen W.|last2=Kumar|first2=Manoj | name-list-style = vanc |title=Nickel-Containing Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase|journal=Chemical Reviews|date=January 1996|volume=96|issue=7|pages=2515–2540|doi=10.1021/cr950058|pmid=11848835}}</ref>

===Other reactions===

It has been discovered that the CODH/ACS enzyme in the bacteria ''M. theroaceticum'' can make [[dinitrogen]] (N{{sub|2}}) from [[nitrous oxide]] in the presence of an [[electron donor|electron-donating species]]. It can also catalyze the [[reductase|reduction]] of the pollutant, [[Trinitrotoluene|2,4,6-trinitrotoluene]] (TNT) and catalyze the [[oxidation]] of [[Butyl group|''n''-butyl]] [[isocyanide]].<ref name="Can, Armstrong Ragsdale review" />

== Structure ==

===History===

The first, and one of the most comprehensive, crystal structures of ACS/CODH from the bacteria ''M. thermoacetica'' was presented in 2002 by Drennan and colleagues.<ref name="Drennan Science magazine">{{cite journal | vauthors = Doukov TI, Iverson TM, Seravalli J, Ragsdale SW, Drennan CL | title = A Ni-Fe-Cu center in a bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase | journal = Science | volume = 298 | issue = 5593 | pages = 567–72 | date = October 2002 | pmid = 12386327 | doi = 10.1126/science.1075843 | bibcode = 2002Sci...298..567D | s2cid = 39880131 }}</ref> In this paper they constructed a heterotetramer, with the active site "A-cluster" residing in the ACS subunit and the active site "C-cluster" in CODH subunit. Furthermore, they resolved the structure of the A-cluster active site and found an [Fe{{sub|4}}S{{sub|4}}]-X-Cu-X-Ni centre which is highly unusual in biology. This structural representation consisted of a [Fe{{sub|4}}S{{sub|4}}] unit bridged to a binuclear centre, where Ni(II) resided in the [[distal]] position (denoted as Ni{{sub|d}}) in a [[square-planar]] conformation and a Cu(I) ion resided in the [[proximal]] position in a distorted [[tetrahedral]] position with [[ligand]]s of unknown identity.<ref name="Drennan Science magazine" />

The debate towards the absolute structure and identity of the metals in the A-cluster active site of ACS continued, with a competing model presented. The authors suggested two different forms of the ACS enzyme, an "Open" form and a "Closed" form, with different metals occupying the [[proximal]] metal site (denoted as M{{sub|p}}) for each form. The general scheme of the enzyme followed closely with the first study's findings, but this new structure proposed a [[nickel]] ion in the "open" form and a [[zinc]] ion in the "closed" form.<ref name="Hegg mechanism ACS" />

A later review article attempted to reconcile the different observations of M{{sub|p}} and stated that this proximal position in the active site of ACS was prone to substitution and could contain any one of [[Copper|Cu]], [[Zinc|Zn]] and [[Nickel|Ni]]. The three forms of this A-cluster most likely hold a small amount of Ni and a relatively larger amount of Cu.<ref name="Drennan, Doukov, Ragsdale">{{cite journal | vauthors = Drennan CL, Doukov TI, Ragsdale SW | title = The metalloclusters of carbon monoxide dehydrogenase/acetyl-CoA synthase: a story in pictures | journal = Journal of Biological Inorganic Chemistry | volume = 9 | issue = 5 | pages = 511–5 | date = July 2004 | pmid = 15221484 | doi = 10.1007/s00775-004-0563-y | s2cid = 23263180 }}</ref>

===Present (2014 onwards)===

[[File:PDB 3I01.jpg|thumb|Bifunctional CODH/ACS unit in ''M.thermoacetica'']]

It is now generally accepted that the ACS active site (A-cluster) is a Ni-Ni metal centre with both nickels having a +2 [[oxidation state]]. The [Fe{{sub|4}}S{{sub|4}}] [[Cluster (chemistry)|cluster]] is bridged to the closer nickel, N{{sub|p}} which is connected via a [[thiolate]] bridge to the farther nickel, Ni{{sub|d}}. Ni{{sub|d}} is coordinated to two [[cysteine]] molecules and two backbone [[amide]] compounds, and is in a [[square-planar]] coordination. The space next to the metal can accommodate substrates and products. Ni{{sub|p}} is in a T-shaped environment bound to three sulfur atoms, with an unknown ligand possibly creating a distorted [[tetrahedral]] environment. This ligand has been hypothesized to be a water molecule or an [[acetyl group]] in the surrounding area in the cell. Although the proximal nickel is labile and can be replaced with a Cu of Zn centre, experimental evidence suggests that activity of ACS is limited to the presence of nickel only. In addition, some studies have shown that copper can even inhibit the enzyme under certain conditions.<ref name="DJ Evans 2005">{{cite journal | last1 = Evans | first1 = David J. | name-list-style = vanc | title = Chemistry relating to the nickel enzymes CODH and ACS|journal=Coordination Chemistry Reviews|date=2005|volume=249|issue=15–16|pages=1582–1595|doi=10.1016/j.ccr.2004.09.012}}</ref>

The overall structure of the CODH/ACS enzyme consists of the CODH enzyme as a [[dimer (chemistry)|dimer]] at the centre with two ACS subunits on each side. The CODH core is made up of two Ni-Fe-S clusters (C-cluster), two [Fe{{sub|4}}S{{sub|4}}] clusters (B-cluster) and one [Fe{{sub|4}}S{{sub|4}}] D-cluster. The D-cluster bridges the two subunits with one C and one B cluster in each monomer, allowing rapid [[electron transfer]]. The A-cluster of ACS is in constant communication with the C-cluster in CODH. This active site is also responsible for the C-C and C-S bond formations in the product acetyl-CoA (and its reverse reaction).<ref name="Drennan, Doukov, Ragsdale" />

Furthermore, the crystal structures of the CODH/ACS complex of ''Carboxydothermus hydrogenoformans'' <ref>{{Cite journal |last=Ruickoldt |first=Jakob |last2=Basak |first2=Yudhajeet |last3=Domnik |first3=Lilith |last4=Jeoung |first4=Jae-Hun |last5=Dobbek |first5=Holger |date=2022-10-21 |title=On the Kinetics of CO 2 Reduction by Ni, Fe-CO Dehydrogenases |url=https://pubs.acs.org/doi/10.1021/acscatal.2c02221 |journal=ACS Catalysis |language=en |volume=12 |issue=20 |pages=13131–13142 |doi=10.1021/acscatal.2c02221 |issn=2155-5435|doi-access=free }}</ref> and ''Clostridium autoethanogenum'' <ref>{{Cite journal |last=Lemaire |first=Olivier N. |last2=Wagner |first2=Tristan |date=January 2021 |title=Gas channel rerouting in a primordial enzyme: Structural insights of the carbon-monoxide dehydrogenase/acetyl-CoA synthase complex from the acetogen Clostridium autoethanogenum |url=https://linkinghub.elsevier.com/retrieve/pii/S0005272820301808 |journal=Biochimica et Biophysica Acta (BBA) - Bioenergetics |language=en |volume=1862 |issue=1 |pages=148330 |doi=10.1016/j.bbabio.2020.148330|doi-access=free |hdl=21.11116/0000-0007-F1AD-6 |hdl-access=free }}</ref> have been solved. While the latter shows a more extended arrangement of the ACS subunits, the complex of ''C. hydrogenoformans'' is very similar to that of ''M. thermoacetica''.

[[File:ACS A cluster active site.jpg|thumb|Acetyl-CoA Synthase active site structure]]

The ACS enzyme contains three main subunits. The first is the active site itself with the NiFeS centre. The second is the portion that directly interacts with CODH in the Wood–Ljungdahl pathway. This part is made up of [[alpha helix|α-helices]] that go into a [[Rossmann fold]]. It also appears to interact with a [[ferredoxin]] compound which may activate the subunit during the CO transferring process from CODH to ACS. The final domain binds CoA and consists of six [[arginine]] residues with a [[tryptophan]] molecule.<ref name="Can, Armstrong Ragsdale review" /><ref name="Drennan current opinion 2011">{{cite journal | vauthors = Kung Y, Drennan CL | title = A role for nickel-iron cofactors in biological carbon monoxide and carbon dioxide utilization | journal = Current Opinion in Chemical Biology | volume = 15 | issue = 2 | pages = 276–83 | date = April 2011 | pmid = 21130022 | doi = 10.1016/j.cbpa.2010.11.005 | url = http://dspace.mit.edu/bitstream/1721.1/71970/1/Drennan_A%20role.pdf | pmc=3061974}}</ref>

Experiments between the C-cluster of CODH and the A-cluster of ACS reveal a long, [[hydrophobic]] channel connecting the two domains to allow for the transfer of carbon monoxide from CODH to ACS. This channel is most likely to protect the carbon monoxide molecules from the outside environment of the enzyme and to increase efficiency of acetyl-CoA production.<ref name="Archives biochem 2014" />

====Conformational changes====

Studies in literature have been able to isolate the CODH/ACS enzyme in an "open" and "closed" configuration. This has led to the hypothesis that it undergoes four conformational changes depending on its activity. With the "open" position, the active site rotates itself to interact with the CFeSP protein in the methyl transfer step of the [[Wood–Ljungdahl pathway]]. The "closed" position opens up the channel between CODH and ACS to allow for the transfer of CO. These two configurations are opposite one another in that access to CO blocks off interaction with CFeSP, and when methylation occurs, the active site is buried and does not allow CO transfer. A second "closed" position is needed to block off water from the reaction. Finally, the A-cluster must be rotated once more to allow for the binding of CoA and release of the product. The exact trigger of these structural changes and the mechanistic details have yet to be resolved.<ref name="Can, Armstrong Ragsdale review" /><ref name="Ragsdale Chem Rev 1996" /><ref name="DJ Evans 2005" />

==Activity==

===Mechanism===

[[File:ACS paramagetic and diamagnetic mechanisms.jpg|thumb|Proposed diamagnetic (top) and paramagnetic (bottom) mechanisms. Adapted from Seravalli et al.<ref name="Seravelli pulse chain study 2008" />]]

Two competing mechanisms have been proposed for the formation of acetyl-CoA, the "[[paramagnetic]] mechanism" and the "[[diamagnetic]] mechanism".<ref name="Can, Armstrong Ragsdale review" /> Both are similar in terms of the binding of substrates and the general steps, but differ in the [[oxidation]] state of the metal centre. Ni{{sub|p}} is believed to be the substrate binding centre which undergoes [[redox]]. The farther nickel centre and the [Fe{{sub|4}}S{{sub|4}}] [[Cluster (chemistry)|cluster]] are not thought to be involved in the process.<ref name="Archives biochem 2014">{{cite journal | vauthors = Boer JL, Mulrooney SB, Hausinger RP | title = Nickel-dependent metalloenzymes | journal = Archives of Biochemistry and Biophysics | volume = 544 | pages = 142–52 | date = February 2014 | pmid = 24036122 | pmc = 3946514 | doi = 10.1016/j.abb.2013.09.002 }}</ref>

In the [[Paramagnetism|paramagnetic]] mechanism, some type of complex ([[ferrodoxin]], for example) activates the Ni{{sub|p}} atom, reducing it from Ni{{sup|2+}} to Ni{{sup|1+}}. The nickel then binds to either [[carbon monoxide]] from CODH or the methyl group donated by the CFeSP protein in no particular order.<ref name="Seravelli pulse chain study 2008">{{cite journal | vauthors = Seravalli J, Ragsdale SW | title = Pulse-chase studies of the synthesis of acetyl-CoA by carbon monoxide dehydrogenase/acetyl-CoA synthase: evidence for a random mechanism of methyl and carbonyl addition | journal = The Journal of Biological Chemistry | volume = 283 | issue = 13 | pages = 8384–94 | date = March 2008 | pmid = 18203715 | pmc = 2820341 | doi = 10.1074/jbc.M709470200 | doi-access = free }}</ref> This is followed by [[migratory insertion]] to form an intermediate complex. CoA then binds to the metal and the final product, acetyl-CoA, is formed.<ref name="Can, Armstrong Ragsdale review" /><ref name="DJ Evans 2005" /> Some criticisms of this mechanism are that it is unbalanced in terms of electron count and the activated Ni{{sup|1+}} intermediate cannot be detected with [[electron paramagnetic resonance]]. Furthermore, there is evidence of the ACS catalytic cycle without any external reducing complex, which refutes the [[ferrodoxin]] activation step.<ref name="Sigel Book 2006 Wiley">{{cite book|last1=Sigel|first1=Astrid|last2=Sigel|first2=Helmut|last3=Sigel|first3=Roland K. O. | name-list-style = vanc |title=Nickel and its surprising impact in nature|date=2006|publisher=Wiley|location=Chichester, West Sussex, England|isbn=978-0-470-01671-8|pages=377–380}}</ref>

The second proposed mechanism, the diamagnetic mechanism, involves a Ni{{sup|0}} intermediate instead of a Ni{{sup|1+}}. After addition of the methyl group and carbon monoxide, followed by [[migratory insertion|insertion]] to produce the metal-acetyl complex, CoA attacks to produce the final product.<ref name="DJ Evans 2005" /> The order in which the carbon monoxide molecule and the methyl group bind to the nickel centre has been highly debated, but no solid evidence has demonstrated preference for one over the other. Although this mechanism is electronically balanced, the idea of a Ni{{sup|0}} species is highly unprecedented in biology. There has also been no solid evidence supporting the presence of a [[zerovalent]] Ni species. However, similar nickel species to ACS with a Ni{{sup|0}} centre have been made, so the [[Diamagnetism|diamagnetic]] mechanism is not an implausible hypothesis.<ref name="Lindahl_2004" />

== References ==
{{reflist|32em}}

{{Acyltransferases}}
{{Enzymes}}
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[[Category:EC 2.3.1]]
[[Category:Enzymes of unknown structure]]