Acetyl-CoA Synthase/ Carbon Monoxide Dehydrogenase (ACS/CODH) A Ni-Fe-S-containing Bifunctional Enzyme with a Bio-organometallic Reaction Mechanism Paul A. Lindahl Departments of Chemistry and Biochemistry/Biophysics Texas A&M University, College Station, TX Where are ACS/CODH’s found? •Anaerobic Bacteria and Archaea •Chemoautotrophic (grows on CO2/H2 or CO) •Evolutionarily primitive (thermophiles) •Major role in global C1 cycle • Three major classes • α2β2 + CoFeSP (γδ) Moorella thermoacetica Methanosarcina thermophila • (αβγδε)2 • β2 Rhodospirillum rubrum Reactions catalyzed by the 310 kDa α2β2 tetramer From Moorella thermoacetica: CO/CO2 Redox (β Subunit): (CODH) CO2 + 2H+ + 2e- CO + H2O Acetyl-CoA Synthesis (α subunit): (ACS) CH3--Co3+FeSP + CO + CoA O CH3-C-SCoA + Co1+FeSP Recombinant α subunit also catalytic if incubate apo-α with Ni Structure of ACS/CODH Alpha Subunit Open Conformation A-Cluster (Active site for ACS reaction) Beta Subunits C-Cluster (Active site For CODH reaction) Doukov et al.,Science 2002 Darnault et al, Nature Structural Biology, 2003 Alpha Subunit Closed Conformation Mechanism of the CODH Reaction Controversy: Role of Bridging Sulfide in C-cluster ? Carboxydothermus hydrogenoformans Dobbek, Svetlitchnyi, Gremer, Huber, Meyer (2001) Science 293, 1281-1285. Moorella thermoacetica Doukov, Iverson, Saravalli, Ragsdale, Drennan, (2002) Science 298, 567-572. Darnault, Volbeda, Kim, Legrand, Vernede, Lindahl, Fontecilla-Camps (2003) Nature Structural Biology 10, 271-279. Proposal of Dobbek, Svetlitchnyi, Liss and Meyer (JACS 2004): •Bridging Sulfide is Required for Activity •Incubation in CO abstracts S, forming COS and inactivating CODH Dithionite, N2 CO + DTT CO Dobbek, Svetlitchnyi, Liss, Meyer J. Am. Chem. Soc., 126 (17), 5382 -5387, 2004. CO + Ti(III)citrate We tried the same experiment… CO Ar Feng and Lindahl J. Am. Chem. Soc., 126 (17), 5382 -5387, 2004. CO + 2MV2+ CO2 + 2MV1+ + 2H+ 0.0 μM HS- •CODHRr incubated in HSthen assayed 0.25 μM HS- •HS- inhibited catalysis 0.50 μM HS- •Inhibition was partial 1.25 μM HS- •Lag phase evident •HS- bound CODH prior to catalysis, Yielding an inhibited state •HS- is expelled, and rebinds during turnover 2.5 μM HS5.0 μM HS10 μM HS100 μM HS- Absorbance due to MV1+ (578 nM) CO Oxidation Activity of CODHRr in the Presence of Sodium Sulfide EPR = Electron Paramagnetic Resonance Can observe systems with S = ½, 3/2, 5/2, etc Ms at E+ = +1/2gβH Axial Symmetry (g║ > g┴) E, Potential Energy ΔE = hυ=gβH S = 1/2 Ms at E- = -1/2gβH Axial Symmetry (g┴>g║) H, Magnetic Field Abs Isotropic Symmetry dAbs dH Quantified by Integration and comparison to Cu(II)EDTA standard Rhombic Symmetry (gx ≠gy ≠gz) H Principal g-value g = hυ/βH (g = 2.0023 for e-) Mixture of Signals Redox, EPR of C-Cluster Anderson et al. Biochemistry, 1996, 8371 -8380 Effect of Sodium Sulfide on Cred1 EPR Spectra Increasing concentrations of sulfide Cred1 signal shifts to g = 1.95, 1.85, 1.70 Cred2 signal does not shift 1 mM HS- Implication for Substrate Binding to C-cluster Effect of HS- on activity and EPR similar to those of CN•Partial Inhibition •Binds Cred1 not Cred2 •CO incubation reactivates Similarity to substrate HO- (ENDOR shows binding to Cred1 not Cred2) Proposal: Substrate HO- binds like HS- --- bridging between [Ni and Fea] in Cred1 only Model of Sulfide Inhibition CO Oxidation Activity of CODHMt with HSFrom the model we can derive the rate equation… 8750 K I + 5190[ HS − ] υ= K I + [ HS − ] Using KI = 60 μM… Jeoung and Dobbek; Science 2007: Structure of the CO2-bound intermediate Observed: •Bridging OH in Cred1 state •CO2 Intermediate •No bridging Sulfide! They Conclude… “…the S2 ligand between Ni and Fe1 is absent in catalytically competent enzyme” “The structure-based mechanism outlined agrees in all central aspects with the bimetallic mechanism proposed on the basis of EPR, ENDOR, and Mössbauer spectroscopy.” CODH Catalytic Mechanism Mechanism of the ACS Reaction: Role of the Tunnel A-Cluster in Open Conformation “Proximal” Nip is labile – can be removed by phen - Reversible Protein Backbone Amide Nitrogens The Fe4S4 Cubane Distal Site, square planar – remains Ni2+ A-cluster in Closed Conformation Cu or Zn can replace Ni in Proximal Site This inactivates the enzyme Tunnel Network in ACS/CODH Closed Conformation Closed Conformation Open Conformation Hydrophobic Tunnel connects A- and C-clusters as well as the two C-clusters In open conformation, tunnel to A-cluster is blocked Tunnel controls delivery of CO to A-cluster ACS Activity vs [CO] 100 ACS/CODH (WT) Plot for ACS/CODH: •At [CO] < 100 μM, CO is a “normal” substrate •At [CO] > 100 μM, CO is an inhibitor •Inhibition is cooperative (more than 1 CO involved) •Residual activity (10% of max) is insensitive to CO -1 v/[Etot](min ) 80 60 Plot for α subunit: •CO is a “normal” substrate •No cooperative inhibition •Max activity is ~ same as residual of WT 40 20 α subunit 0 0 200 400 600 [CO] (μM) 800 1000 Effect of Blocking Tunnel Tan, Loke, Fitch, and Lindahl, J. Am. Chem. Soc. 2005 Tan, Volbeda, Fontecilla-Camps, Lindahl, JBIC 2006 Blockage between A and C-clusters: CODH activity unaffected ACS activity (using CO2) ~ 0 ACS activity using CO – residual only No CO-cooperative inhibition Blockage between C and C-clusters: Same as AC mutants but CODH activity ~ 5% of WT CO/CO2 may enter at beta:beta interface Two Migration Pathways for CO used in ACS Catalysis Tunnel Pathway: CO enters at the ββ interface and migrates to the A-cluster Responsible for majority activity and CO cooperative inhibition Direct-binding Pathway: CO from solvent binds Nip of the A-cluster directly. Responsible for the residual activity Not associated with CO cooperative inhibition Conclusions • The tunnel delivers CO/CO2 to the active sites; delivery is regulated by protein conformational change • The tunnel region between A- and C-clusters is exclusively used for ACS reaction, not CODH reaction • The tunnel region between the two C-clusters participates in the CODH reaction (and indirectly in the ACS reaction) • CO/CO2 may enter/exit the enzyme at the β-β interface • The tunnel is involved in the cooperative inhibition by CO • CO used in “majority” activity approaches Nip via tunnel • CO used in residual activity approaches Nip via solvent Mechanism of the ACS Reaction: Electronic Configuration of the A-cluster Mössbauer Spectroscopy (Nuclear γ-Ray Resonance) Useful for 57Fe (I = ½) Systems All electronic and magnetic states observed (no “Mössbauer-Silent Fe) Intensity proportional to # of Fe atoms contributing ΔEQ I = 3/2 14.4 KeV δ= isomer shift (0 mm/s) (0.2–1 mm/s) Magnetic; e.g. 60% Connected to EPR 40% Quadrupole Doublet I = 1/2 Change in Oxidation State Change in Symmetry Magnetic Field (external Or Internal e.g. S = 1/2) 0 % Transmission Energy (mm/s) “Quadrupole Doublet”“Magnetic” Rhombic symme Or Magnetic Mixture Redox States of the A-cluster Aox State Obtained when potential > -500 mV vs. NHE No EPR Signals (i.e. not Ni1+ or Ni3+); Nip is 2+ Mössbauer shows quadrupole doublet typical of S = 0 [Fe4S4]2+ Electronic Assignment: Aox = {[Fe4S4]2+ Nip2+} Ssystem = 0 CH3-Aox: Methylated State Mössbauer shows S = 0 [Fe4S4]2+ EPR silent (i.e. not Ni1+ or Ni3+) i.e. Nip2+ Many examples of Ni2+-CH3 model complexes Nip is required for methyl transfer; methylation blocks Nip removal Electronic Assignment: CH3-Aox = {[Fe4S4]2+ Nip2+-CH3} Ssystem = 0 Bramlett et al, Biochemistry, 2006 Ared-CO State Aox + 1e- + CO S=0 ֎ Ared-CO S=1/2 NiFeC EPR signal (g┴ = 2.08, g║= 2.03) Mössbauer shows magnetic [Fe4S4]2+ Electronic Assignment: Ared-CO = {[Fe4S4]2+ Nip1+-CO} Catalytic Intermediate or Inhibitor of catalysis? Bramlett et al, Biochemistry, 2006 Ared-Act: The Reductively Activated State Aox + CH3-Co3+FeSP No Reaction But in presence of low-potential reductant (e.g. dithionite, Ti3+ citrate)… (Aox+ ne-} + CH3-Co3+FeSP CH3-A + Co1+FeSP 390 nm Ti(III) citrate Dithionite Phen-Treated No Reductant Mechanistic Implications Step 1: Reductive Activation: {[Fe4S4]2+ Nip2+} + neSsystem = 0 (or 1) Step 2: Methylation: Ared-act {?} + CH3+ Ared-act {?} {[Fe4S4]2+ Nip2+-CH3} Implications: Ssystem for Ared-act = 0 (or 1, 2 etc) and n=2 Ssystem = 0 (or 1) Steps 3 and 4: CO Insertion, CoASH attack: {[Fe4S4]2+ Nip2+-CH3} + CO + CoASH Ared-act {?} Acetyl-CoA The Heterogeneity Puzzle: For all labs, enzymes, preps… Spin concentration of NiFeC EPR signal 0.2 - 0.3 spin/α Quantification of methyl group transfer: 0.3 – 0.5 Me/α Quantification of labile Ni removed and inserted: ~ 0.2 Ni/α Mössbauer of Ared-CO: ~30% is S = ½ [Fe4S4]2+; ~70% is S = 0 [Fe4S4]2+ What does this mean? ~ 30% functional α subunits •Catalytically active •Labile Ni • capable of NiFeC EPR ~70% nonfunctional α subunits * inactive * no labile Ni (Zn? Cu?) 4.2 K Mössbauer Spectra of α; ca. 2006 apo-α+ dithionite For Ared-act: ~ 30% S = 0 [Fe4S4]2+ (functional form) Ni-α+ Ti(III)citrate (Ared-act) ~ 70% S = 3/2 [Fe4S4]1+ (nonfunctional form) Heterogeneity present In apo-alpha form Ni-α+ dithionite + CO (Ared-CO) ~30% Ared-CO Bramlett, Stubna, Tan, Surovtsev, Munck, Lindahl, Biochemistry 2006 Conclusions Regarding Ared-act 70% Component represents nonfunctional A-clusters {[Fe4S4]1+ X} 30% Component represents functional A-clusters Ared-act = S = 0, {[Fe4S4]2+ Nip0} Objections to a Nip0 State Ligands are inconsistent (not phosphines) But bridging thiolates might mimic phosphines… Shouldn’t a zero-valent Ni reduce [Fe4S4]2+? But Mössbauer study suggests E0cube2+/1+ < -800 mV Two DFT computational studies disfavor {[Fe4S4]2+ Nip0} state. But E0 is very sensitive to environment ∴ difficult to model accurately Two redox titrations suggest n = 1 (not n = 2) for reductive activation 15 Refitting of Data of Bhaskar, DeMoll, and Grahame, Biochemistry, 1998, 37, 14491-4499 pH 6.5 pH 7.9 pH 7.2 pH 6.5 Previously reported n = 1 fit to Nernst Equation pH 7.2 10 Activity Our refitting (2-term global optimization) Best-Fit values: n = 1.7±0.2 E0 = -479 (pH 6.5) E0 = -495 (pH 7.2 ) E0 = -524 (pH 7.9) 5 pH 7.9 0 -640 -560 -480 Redox potential, mV -400 Shouldn’t the Fe4S4 be reduced in Ared-act?? Let’s monitor reduction of [Fe4S4]2+ cubane by Ti3+ citrate… Reduction is slow relative to methylation rate (Nonfunctional form is probably becoming reduced) Tan…Lindahl, JACS 2003 Competition Experiment: CH3-Co3+FeSP and Ti3+citrate αox (Add reductant and CH3-Co3+FeSP Simultaneously to αox) Monitor at 390 nm (sensitive to both [Fe4S4]2+ reduction and Co1+) CH3 transfer (and reductive activation) > 100X faster than cubane reduction Cubane NOT reduced fast enough to be the site of reductive activation But heterogenity could complicate interpretation… A-cluster model complexes support n = 2, Nip0 –based Mechanism Ito, Kotera, Matsumoto, Tatsumi (PNAS, 2009) [Nid2+ Nip0] Ared-act [Nid2+ Nip2+-CH3] CH3-Aox Also… Riordan, Rauchfuss, Holm, Darensbourg, Mascharak Structurally Relevant Model Complexes display same essential chemistry! In 2007, we stopped adding Ni to E coli and started running α on FPLC (FPLC; Superdex gel filtration) A apo-α 88% monomer 12% dimer apo-α + Ni B 15% monomer 38% dimer 47% tetramer dimer peak; C Concentrated, Re-run 0 20 40 48% monomer 49% dimer 3% tetramer 60 80 Time, min 100 Dimer and tetramer have Activity; not monomer Dimer: 0.5 Me/α transferred 0.4 spin/ α NiFeC spin intensity Dimer is heterogeneous (one functional subunit; one nonfunctional subunit) 120 (Tan, Kagiampakis, Surovtsev, Demeler, Lindahl, Biochemistry 2007) Properties of Ni-activated Alpha Subunit Dimers A Methyl Group Acceptor Ability: Dimer accepts ~ 0.5 Me/α Monomer ~ inactive B 0.04 Why only 0.5 Me/α? Incomplete Reaction? Change [α] and see if Me/α changes 20 μM 10 μM 5 μM 2.5 μM 1.5 μM ~ 0.5 Me/α at all [α] What does this mean? Relative Abs change 0.02 C D 0.00 0.08 E 0.06 F 0.04 0.02 0.00 0.00 G H L 0.25 0.50 Time (S) 0.75 1.00 Asymmetric Subunits in Ni-activated Dimer EPR of reduced/CO dimer: NiFeC signal had 0.4 spin/α (EPR of monomer apo-α showed only residual signal) Mössbauer Spectra of reduced/CO dimer: 40% associated with S = ½ Ared-CO state 60% associated with S = 0 [Fe4S4]2+ inactive clusters When considered with methyl group transfer quantification, (0.5 Me/α) Indicates that alpha dimers consist of asymmetric subunits * One “catalytic” subunit (accepts Me group; exhibits NiFeC) * One “structural” subunit Could heterogeneity be functionally required?? Is Dimerization Specific for Ni? NiA2+ Dimer Cu2+ B Zn2+ C Co2+ Higher-Mol. Wt Oliogmer D Monomer Pd2+ E Dimer PtF2+ 0 20 40 60 80 100 Min/ml 120 140 160 180 Tentative Conclusions Regarding Dimerization Alpha subunits dimerize when Ni binds to the proximal site of the A-cluster Dimerization (Oligomerization) is specific for M2+ ions that prefer square-planar geometries (Ni, Pd, Pd) This geometry at the proximal site enforces a particular subunit conformation (i.e. open) that is conducive to dimerization One subunit of the dimer is catalytic and in the open conformation while the other is structural and in the closed conformation Apo-α + Ti(III) citrate ca. 2008 ~ 100% is S = 1/2 [Fe4S4]1+ cluster – no redox heterogeneity 4.2 K Mössbauer of [α(Ni)]2 + Ti(III) Citrate 20% S = ½ [Fe4S4]1+ 52% S = 0 {[Fe4S4]1+ Ni1+} 22% S = 0 {Fe4S4]1+ Ni1+} δ = 0.56 mm/s ΔEQ = 1.25 mm/s δ = 0.55 mm/s ΔEQ = 0.47 mm/s Coupled state proposed by Brunold and Field, based on DFT Tan et al.,, J. Am. Chem. Soc. 2008 4.5 K 0.05T Mössbauer of A-Cluster containing subunit from Methanosarcina thermophila Aox state ~100% S = 0 [Fe4S4]2+ (δ = 0.46 mm/s; ΔEQ = 1.1 mm/s) Ared-act state ~80% S = 0 {[Fe4S4]2+Nip2+/0} (δ = 0.46 mm/s; ΔEQ = 1.1 mm/s) ~20% S = 0 {[Fe4S4]1+ Nip1+} (δ = 0.53 mm/s; ΔEQ = 1.1 mm/s) Sample was ~ 100% active in accepting methyl group Kinetic Model for the ACS Reaction: Kinetic Modeling of the Acetyl-CoA Synthesis Mechanism Tan, Surovtsev, Lindahl, JACS 2007 Monitoring the Kinetics of Methyl Group Transfer – Relatively Easy CH3-Co3+ Ni0 (in Ti3+) Ni 2+ -CH 3 + Co1+ Ni 0 + CH 3 -Co3+ ⇄ k+ met = 15 μ M s −1 −1 k− met < 0.05 μ M −1s −1 K met > 300 A Absorbance Monitoring the Thermodynamics of CO Insertion - not so easy 0.72 CO = 0 μM CO = 0.5 μM 0.68 CO = 1 μM CO = 5 μM 0.0 0.2 Time, s 0.3 0.4 B 75 v0, μM s -1 Ni2+-C(O)CH3 50 KD(ins)= 0.3 μM 25 0 0 1 2 3 CO concentration, μM Ni2+0.36 -C(O)CH3 + Co1+ Absorbance Co1+ CO Ni2+-CH3 0.1 ⇅ 4 ⇄ No Reaction CO + 0.0 C k+ins= 100 k+ins= 1 0.34 Ni2+-CH3 5 CO = 0 μM 0.2 0.4 ⇌ 0.6 k+ins= 0.1 CO = 20 μM 0.8 1.0 + Co1+Time, sNi0 + CH3-Co3+ A Absorbance Competition Reaction to Monitor Kinetics of CO Insertion 0.72 - More difficult CO = 0 μM CO = 0.5 μM 0.68 CO = 1 μM CO = 5 μM 0.0 0.1 0.3 0.4 ⇄ 75 v0, μM s -1 Ni2+-CH3 + Co1+ Ni0 + CH3-Co3+ 50 + KD(ins)= 0.3 μM CO 25 CO + Co1+ B k+ins 0 Ni2+-C(O)CH 0 13 Absorbance Ni2+-CH3 0.2 Time, s 2 3 4 5 -1 -1 When k = 100 μM s +ins CO concentration, μM Not a good fit C 0.36 k+ins= 100 k+ins= 1 0.34 CO = 0 μM k+ins= 0.1 CO = 20 μM k+ins= 0.1 μM-1s-1 0.0 0.2 0.4 0.6 Time, s 0.8 1.0 Monitoring Acetyl Group Transfer - Difficult ⇄ Ni:CO CoA + CH3-Co3+ Ni2+ -C(O)CH3 CO Ni 2+ -C(O)CH 3 + CoA ⇄ Ni 0 + CH 3C(O)-CoA + CH 3 -Co3+ Use methyl Transfer Rxn as a reporter ↓ Ni 2+ -CH 3 + Co1+ (detect this) Incubate Ni2+-CH3 + CO Works – but simulations must include CO inhibition ACoA,1000 μM; CO, 20 μM 0.48 CoA,100 μM; CO, 20 μM B CoA,10 μM; CO, 20 μM C Absorbance 0.46 CoA,1000 μM; CO, 40 μM 0.44 D 0.42 Best-Fit Kinetic Parameters k+ CoA = 4 μM −1s −1 0.0 0.1 0.2 0.3 Time, s 0.4 k− CoA = 6 μM −1s −1 0.5 0.6 K CoA = 0.66 k+ CO = 12 μM −1s −1 k− CO = 65 s −1 K CO = 0.19 μM −1 Predictions of Model… Ni 0 + CH 3 -Co3+ FeSP Ni 2+ -CH 3 + CO Ni 2+ -C(O)CH 3 + CoA ⇄ ⇄ ⇄ Ni 2+ -CH 3 + Co1+ FeSP K met Ni 2+ -C(O)CH 3 K ins CH 3C(O)-CoA + Ni 0 K CoA CO + CoA + CH 3 -Co3+ FeSP ⇄ CH 3 -C(O)-CoA + Co1+ FeSP K met ⋅ K ins ⋅ K CoA = K ACS K ACS 100 Actual lower limit KACS > 0.03 μM-1 Acetyl-CoA, μM > 300 ⋅ 3.3μ M −1 ⋅ 0.66 = > 660μ M −1 50 0 0 300 600 Time, s 900 1200 Predictions of the Model… -1 kcat, min Simulated effect of CO shows inhibition effect similar to that observed experimentally 150 100 50 0 Simulation 0 200 400 600 800 CO, μM 100 1.0 A 80 0.8 Ni:CO -1 v/[Etot](min ) Data 1000 0.6 60 40 0.4 20 B 0 0.0 0 0.2200 0.4400 0.6600 Time, [CO ] s( μ M ) 0.8800 1.0 1000 k Seravalli, Kumar, Ragsdale Biochemistry 2002 50 0 0 200 400 600 800 1000 CO, μM 1.0 A Ni:CO 0.8 0.6 CH3-Co3+ +CO+CoA Ni:CO 0.4 Nonzero steady-state said to “prove” Intermediacy of Ni:CO state B 0.0 0.2 0.4 0.6 Time, s 0.8 1.0 Simulation shows decay of inhibitory Ni:CO state reaching a non-zero steady-state upon reacting with CH3-Co3+, CO and CoA as observed experimentally Predictions of the Model… Distribution of Enzyme States During Steady-State Catalysis Fixed conditions as commonly used Calculated % in each intermediate state Found: Ni0, Ni2+-CH3 Ni2+-C(O)CH3 Ni:CO 0.2% 95% 0.3% 4.4% According to these computations, CO Insertion is Rate Limiting Step Sensitivity Analysis Rate Coefficient k Δυ0 / υ0 Δk / k k+met 0.339 k-met -0.002 k+ins 0.657 k-ins -0.0004 k+CoA 0.002 k-CoA 0.001 k+CO -0.332 k-CO 0.317 Acetyl-CoA Synthesis Mechanism (circa May 2006) Conclusions ACS/CODH catalyzes the synthesis of Acetyl-CoA from CO, CoA And a methyl group donated by a corrin protein Active site A-cluster is a novel {[Fe4S4]-Nip Nid} cluster. Aox: {[Fe4S4]2+ Nip2+ Nid2+} Ared-act: {[Fe4S4]2+ Nip0 Nid2+} or {[Fe4S4]1+ Nip0 Nid2+} CH3-Aox: {[Fe4S4]2+ Nip2+-CH3 Nid2+} Heterogeneity and batch-to-batch variations cause confusion Ni-dependent oligomerization Chemical kinetic study: • reductive activation • Methyl group transfer • CO insertion (slow step, probably involves protein conf. change) • CoA attack, forming product Acknowledgements Texas A&M Drs. Xiangshi Tan and Ivan Surovtsev Matthew Bramlett, Huay-Keng Loke, Ernie Maynard, David Barondeau, Woonsup Shin Collaborators Eckard Münck and Audria Stubna (Carnegie Mellon) Juan Fontecilla-Camps and Anne Volbeda (Grenoble) David Grahame (Uniformed Services University of the Health Sciences) Funding National Institutes of Health