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Review
. 2014 Apr 23;114(8):4149-74.
doi: 10.1021/cr400461p. Epub 2014 Feb 13.

Structure, function, and mechanism of the nickel metalloenzymes, CO dehydrogenase, and acetyl-CoA synthase

Mehmet Can  1 , Fraser A Armstrong, Stephen W Ragsdale
Affiliations
Review

Structure, function, and mechanism of the nickel metalloenzymes, CO dehydrogenase, and acetyl-CoA synthase

Mehmet Can et al. Chem Rev. .
No abstract available

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Figures

Figure 1
Figure 1
The Wood–Ljungdahl pathway of CO/CO2 fixation and its involvement in acetogenesis and methyltrophy, as well as in the oxidation of acetate to methane. The methanogenic CODH/ACS is often called ACDS, acetyl-CoA synthase decarbonylase.
Figure 2
Figure 2
(A) Structure of CODHRr in cartoon representation, (B) distances between the metal clusters, (C) structure of the D-cluster, (D) structure of the B-cluster, and (E) structure of the C-cluster. Atom colors: dark gray (iron), orange (sulfide), red (oxygen), blue (nitrogen), white (carbon), dark green (nickel). Generated using Pymol from PDB 1JQK.
Figure 3
Figure 3
Structure of C-cluster including only one coordinating residue, cysteine, and the ligands from (A) CODHRr (PDB 1JQK), (B) CODHCh II (PDB 1SU8), (C) CODHCh II at 320 mV (PDB 3B53), (D) CODHCh II at 600 mV (PDB 3B51), (E) cyanide-bound CODHCh II at 320 mV (PDB 3I39), (F) CO2-bound CODHCh II at 600 mV (PDB 3B52), (G) cyanide-bound CODH/ACSMt (PDB 3I04), (H) CODH/ACSMt (PDB 3I01), (J) n-BICt-bound CODH/ACSMt (PDB 2YIV), (K) CO-bound CODHMb (PDB 3CF4). Atom colors: Dark gray (iron), orange (sulfide), red (oxygen), blue (nitrogen), white (carbon), dark green (nickel).
Scheme 1
Scheme 1. Mechanism of the Water–Gas Shift Reaction
Scheme 2
Scheme 2. Proposed Catalytic Mechanism of Reversible Carbon Monoxide Dehydrogenase
The most well-characterized ferredoxin (Fd) from M. thermoacetica and many other organisms contains two [Fe4S4] clusters and thus can accept two electrons. For a Fd containing a single cluster, two Fd would be required.
Figure 4
Figure 4
Structure of the C-cluster from CODHCh II at 600 mV including only one coordinating residue: histidine and the ligands proposed to be important in catalytic activities. Atom colors: Dark gray (iron), orange (sulfide), red (oxygen), blue (nitrogen), white (carbon), dark green (nickel). Unbound red spheres represent the water molecules. Generated using Pymol from PDB 3B51.
Scheme 3
Scheme 3. Schematic Views of Model Complexes Mimicking the C-Cluster
Scheme 4
Scheme 4. Schematic View of the Proposed Intermediates in CO2 Reduction on Palladium Catalyst
Figure 5
Figure 5
Protein film voltammograms showing CO2 reduction and CO oxidation activities of CODHCh I adsorbed on a PGE electrode under atmospheres of 100% CO2, 100% CO, or 1:1 CO2/CO gas mixtures. Scan rate was 10 mV/s in parts a, c, and d and 30 mV/s in part b. Electrode rotation 4000 rpm. Reprinted with permission from ref (45a). Copyright 2007 American Chemical Society.
Figure 6
Figure 6
Voltammograms showing, for CODHCh I, (A) the potential dependence of inhibition of CO2 reduction activity upon injection of cyanide (CO oxidation is completely inhibited), pH 7.0, scan rate 1 mV s–1 and (B) inhibition of CO2 reduction activity and shift in potential for CO oxidation upon addition of cyanate, pH 7.0, scan rate 1 mV s–1. Adapted with permission from ref (45b). Copyright 2013 American Chemical Society.
Figure 7
Figure 7
Potential dependence of binding of inhibitors to CODHCh I. Red refers to the potential region over which the enzyme is inhibited, gray indicates no binding, and green indicates that binding leads to turnover. The dashed arrows indicate reactions that are slow compared to those indicated by full arrows. Reprinted with permission from ref (45b). Copyright 2013 American Chemical Society.
Scheme 5
Scheme 5. Summary of the Interceptions of the Catalytic Cycle of CODHCh I by Small Molecule Inhibitors, As Deduced from PFE Experiments
The potentials −250 and −50 mV are the values observed for reactivation of enzyme with and without sulfide. The potential −520 mV is the standard potential for the CO2/CO half-cell reaction at pH 7.0. Reprinted with permission from ref (45b). Copyright 2013 American Chemical Society.
Figure 8
Figure 8
(A) Cartoon representation of an enzymatic device for catalysis of the water–gas shift reaction. Electrons released by CODH-catalyzed CO oxidation are transferred through a graphite particle to a CO-tolerant hydrogenase that reduces protons to H2. (B) Typical cyclic voltammograms (from separate experiments) showing the reversibility of electrocatalysis by CODHCh I and a hydrogenase (Hyd-2) from E. coli, measured at pH 6.0, 30 °C, scan rate 10 mV s–1, electrode rotation rate 2500 rpm. (C) H2 production and CO depletion over the course of 55 h at pH 6.0, 30 °C, as quantified by GC analysis. Fresh aliquots of CO were introduced at the times indicated. Adapted with permission from ref (51). Copyright 2009 American Chemical Society.
Figure 9
Figure 9
Photoelectrocatalysis of CO2 reduction to CO catalyzed by CODH attached to light-harvesting nanoparticles. (A) The concept: red arrows correspond to injection of electron into the conduction band (potential ECB) by a photosensitizer (RuP) attached to the nanoparticle; green arrows correspond to injection of electron into the conduction band by band gap excitation (potential difference EG) from the valence band (potential EVB). The hole in either dye or valence band must be filled more rapidly than the electron can return (the electron–hole recombination rate). (B) Production of CO by visible light using a photosensitizer. Experiments carried out by irradiating a vial containing a 5 mL suspension of various semiconducting nanoparticles with visible light (λ > 420 nm). In each case, 5 mg of nanoparticles (20 mg in the case of ZnO) was modified with CODHCh I (total 2.56 nmol) and RuP (total 56 nmol). The buffer in each experiment was 0.20 M MES, pH 6, 20 °C. (C) Production of CO by visible light using direct band gap excitation of various types of cadmium sulfide attached to CODHCh I. QD = quantum dot, NR = nanorod; calcined CdS was heated at 450 °C for 45 min. The buffer in each experiment was 0.35 M MES, pH 6, at 20 °C. Adapted from refs (146a) (copyright 2011 The Royal Society of Chemistry) and (147) (copyright 2012 The Royal Society of Chemistry) with permission.
Figure 10
Figure 10
Structure of CODH/ACSMt. (A) Overall structure of CODH/ACS. Green units in the center are the two CODH homodimers; the left unit is the ACS in open conformation, and the right unit is the ACS in closed conformation. Closer views of the A-cluster pocket in (B) open conformation and (C) closed conformation. Atom colors: Brown (iron), orange (sulfide), red (oxygen), blue (nitrogen), light green (carbon), dark green (nickel), white (unassigned). Generated using Pymol from PDB 1OAO.
Figure 11
Figure 11
Structure of A-cluster from PDB (A and B) 1OAO, (C) 1MJG, and (D) 2Z8Y. Generated using Pymol.
Figure 12
Figure 12
Structure of CODH/ACSMt crystallized in the presence of high pressures of Xe (PDB 2Z8Y) (shown as the blue spheres) to reveal the hydrophobic CO tunnel. Adapted with permission from ref (71e). Copyright 2008 American Chemical Society.
Scheme 6
Scheme 6. Proposed Paramagnetic Mechanism of Acetyl-CoA Synthesis Catalyzed by the A-Cluster
Scheme 7
Scheme 7. Schematic Views of Model Complexes of A-Cluster
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