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- PDB-9g7i: Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (C... -

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Basic information

Entry
Database: PDB / ID: 9g7i
TitleStructure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with acetyl-Coenyzme A from Clostridium autoethanogenum
Components
  • CO-methylating acetyl-CoA synthase
  • Carbon monoxide dehydrogenase
KeywordsOXIDOREDUCTASE / Carbon monoxide / acetyl-CoA / Wood-Ljungdahl pathway / C-cluster / A-cluster / gas channelling / acetogenic bacteria
Function / homology
Function and homology information


CO-methylating acetyl-CoA synthase / CO-methylating acetyl-CoA synthase activity / anaerobic carbon-monoxide dehydrogenase activity / acetyl-CoA metabolic process / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Carbon monoxide dehydrogenase subunit alpha ,N-terminal / Carbon monoxide dehydrogenase subunit alpha N-terminal domain / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / Bifunctional carbon monoxide dehydrogenase/acetyl-coa synthase, domain 3 superfamily / CO dehydrogenase/acetyl-CoA synthase complex beta subunit , C-terminal / CO dehydrogenase/acetyl-CoA synthase complex beta subunit / ACS/CODH beta subunit C-terminal / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily
Similarity search - Domain/homology
ACETYL COENZYME *A / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / IRON/SULFUR CLUSTER / FE(4)-NI(1)-S(4) CLUSTER / CO-methylating acetyl-CoA synthase
Similarity search - Component
Biological speciesClostridium autoethanogenum DSM 10061 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsLemaire, O.N. / Yin, M.D. / Murphy, B.J. / Wagner, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)DFG-SPP 1927 WA 4053/1-1 Germany
CitationJournal: Science / Year: 2025
Title: Conformational dynamics of a multienzyme complex in anaerobic carbon fixation.
Authors: Max Dongsheng Yin / Olivier N Lemaire / José Guadalupe Rosas Jiménez / Mélissa Belhamri / Anna Shevchenko / Gerhard Hummer / Tristan Wagner / Bonnie J Murphy /
Abstract: In the ancient microbial Wood-Ljungdahl pathway, carbon dioxide (CO) is fixed in a multistep process that ends with acetyl-coenzyme A (acetyl-CoA) synthesis at the bifunctional carbon monoxide ...In the ancient microbial Wood-Ljungdahl pathway, carbon dioxide (CO) is fixed in a multistep process that ends with acetyl-coenzyme A (acetyl-CoA) synthesis at the bifunctional carbon monoxide dehydrogenase/acetyl-CoA synthase complex (CODH/ACS). In this work, we present structural snapshots of the CODH/ACS from the gas-converting acetogen , characterizing the molecular choreography of the overall reaction, including electron transfer to the CODH for CO reduction, methyl transfer from the corrinoid iron-sulfur protein (CoFeSP) partner to the ACS active site, and acetyl-CoA production. Unlike CODH, the multidomain ACS undergoes large conformational changes to form an internal connection to the CODH active site, accommodate the CoFeSP for methyl transfer, and protect the reaction intermediates. Altogether, the structures allow us to draw a detailed reaction mechanism of this enzyme, which is crucial for CO fixation in anaerobic organisms.
History
DepositionJul 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CO-methylating acetyl-CoA synthase
B: Carbon monoxide dehydrogenase
C: Carbon monoxide dehydrogenase
D: CO-methylating acetyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,70379
Polymers289,9374
Non-polymers7,76575
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)298.077, 298.077, 127.526
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 2 types, 4 molecules ADBC

#1: Protein CO-methylating acetyl-CoA synthase / Carbon monoxide dehydrogenase/acetyl-CoA synthase complex / alpha subunit


Mass: 76991.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Clostridium autoethanogenum DSM 10061 (bacteria)
Cell line: / / Organ: / / Plasmid details: / / Variant: wild type / Strain: DSM 10061 / Tissue: /
References: UniProt: F8TEQ9, CO-methylating acetyl-CoA synthase
#2: Protein Carbon monoxide dehydrogenase


Mass: 67977.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Clostridium autoethanogenum DSM 10061 (bacteria)
Cell line: / / Organ: / / Plasmid details: / / Variant: wild type / Strain: DSM 10061 / Tissue: / / References: anaerobic carbon monoxide dehydrogenase

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Non-polymers , 12 types, 89 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#10: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-XCC / FE(4)-NI(1)-S(4) CLUSTER / C CLUSTER


Mass: 410.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.74 Å3/Da / Density % sol: 74.08 % / Description: brown square plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystallization was performed anaerobically by initial screening at 20 degrees Celsius using the sitting drop method on 96 Well MRC 2 Drop polystyrene Crystallization Plates SWISSCI in a Coy ...Details: Crystallization was performed anaerobically by initial screening at 20 degrees Celsius using the sitting drop method on 96 Well MRC 2 Drop polystyrene Crystallization Plates SWISSCI in a Coy tent containing an N2/H2 (97:3%) atmosphere. The reservoir contained 90 ul of 25 % (w/v) glycerol ethoxylate 1,000, 100 mM Tris/HCl pH 8.5, and 100 mM CaCl2. 0.6 ul of crystallization solution was mixed with 0.6 ul of the protein, containing a final concentration of 2 mM acetyl-CoA. The protein was concentrated at 15 mg/ml in 25 mM Tris/HCl pH 7.6, 10% (v/v) glycerol, and 2 mM dithiothreitol. The crystals appeared in few weeks and were soaked in the crystallization solution supplemented with 15% (v/v) Ethylene glycol for a few seconds before freezing in liquid nitrogen.
PH range: / / Temp details: /

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.93→59.61 Å / Num. obs: 99666 / % possible obs: 96.1 % / Redundancy: 22.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.045 / Rrim(I) all: 0.211 / Rsym value: 0.045 / Net I/σ(I): 14.5
Reflection shellResolution: 2.93→3.16 Å / Redundancy: 23.3 % / Rmerge(I) obs: 2.423 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4983 / CC1/2: 0.593 / Rpim(I) all: 0.513 / Rrim(I) all: 2.477 / Rsym value: 0.513 / % possible all: 73

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.93→49.68 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.23 / Stereochemistry target values: ML
Details: The structure was refined with phenix.refine considering translation libration screw. Riding hydrogens and non-crystallography symmetry were not used during the refinement.
RfactorNum. reflection% reflection
Rfree0.2202 5002 5.02 %
Rwork0.1902 --
obs0.1917 99636 81.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 89.64 Å2
Refinement stepCycle: LAST / Resolution: 2.93→49.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20122 0 342 14 20478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0120780
X-RAY DIFFRACTIONf_angle_d1.36728075
X-RAY DIFFRACTIONf_dihedral_angle_d15.8557736
X-RAY DIFFRACTIONf_chiral_restr0.093264
X-RAY DIFFRACTIONf_plane_restr0.0063566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.93-2.970.336250.345160X-RAY DIFFRACTION2
2.97-30.3515140.3644304X-RAY DIFFRACTION8
3-3.040.4075380.3483654X-RAY DIFFRACTION17
3.04-3.080.3064510.327970X-RAY DIFFRACTION25
3.08-3.120.3511780.31021265X-RAY DIFFRACTION33
3.12-3.160.3234990.30291669X-RAY DIFFRACTION44
3.16-3.210.32631150.28882107X-RAY DIFFRACTION55
3.21-3.250.33281310.29142639X-RAY DIFFRACTION69
3.25-3.30.3291770.28363240X-RAY DIFFRACTION85
3.3-3.360.30721980.26733787X-RAY DIFFRACTION98
3.36-3.420.30712100.24983827X-RAY DIFFRACTION100
3.42-3.480.28891900.24233826X-RAY DIFFRACTION100
3.48-3.550.29722070.23643853X-RAY DIFFRACTION100
3.55-3.620.27022050.22363827X-RAY DIFFRACTION100
3.62-3.70.23022020.21083863X-RAY DIFFRACTION100
3.7-3.780.24262090.19893842X-RAY DIFFRACTION100
3.78-3.880.22641910.19073889X-RAY DIFFRACTION100
3.88-3.980.19162060.1783851X-RAY DIFFRACTION100
3.98-4.10.19852210.16353841X-RAY DIFFRACTION100
4.1-4.230.17711990.16043857X-RAY DIFFRACTION100
4.23-4.380.17612010.14923903X-RAY DIFFRACTION100
4.38-4.560.1941860.1473892X-RAY DIFFRACTION100
4.56-4.760.18171870.14253899X-RAY DIFFRACTION100
4.76-5.020.19822160.14813877X-RAY DIFFRACTION100
5.02-5.330.21452310.1683892X-RAY DIFFRACTION100
5.33-5.740.19462040.18293903X-RAY DIFFRACTION100
5.74-6.320.23431930.20033957X-RAY DIFFRACTION100
6.32-7.230.20332210.19693944X-RAY DIFFRACTION100
7.23-9.10.18182030.17334014X-RAY DIFFRACTION100
9.1-49.680.21212140.19354182X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9373-0.298-0.84940.82590.29421.8754-0.1522-0.32760.09550.15330.1389-0.1499-0.40960.0912-0.00790.67580.16060.05240.36570.06830.530497.751251.321143.9543
25.42261.14162.09744.0182.77555.1382-0.29430.1273-0.36910.4509-0.02771.17360.2935-1.23350.30880.7320.21750.40071.09970.25561.17460.485535.172340.7864
31.8943-0.44-0.28391.50591.13770.86-0.0163-0.0065-0.3076-0.09420.0080.6646-0.0884-0.78520.00250.48080.15180.14280.58630.08110.761374.134937.814528.5016
40.5201-0.49190.47520.696-0.31540.4679-0.2136-0.382-0.03890.3630.24630.4417-0.4293-0.3446-0.10660.76310.30340.270.65760.07710.690778.240147.043149.8076
52.9269-0.0550.21712.9319-0.51841.7727-0.2985-0.5763-0.1881.16290.36250.2217-0.0238-0.2113-0.05680.93110.41240.24770.8140.14160.644283.19144.63964.6389
62.0476-0.85620.21111.3923-0.40071.4685-0.1912-0.08650.30830.24930.11550.1292-0.3378-0.10080.05070.68250.21240.13520.35310.01250.634476.690661.822635.4249
72.56490.1126-0.72892.9141-0.20141.7860.18390.21350.291-0.037-0.11940.3343-0.1687-0.3695-0.06610.76830.32950.09140.53840.06930.871647.981486.592824.2458
83.9526-0.109-0.47733.57220.64562.91620.1365-0.3785-0.26120.4089-0.10640.55770.43620.00270.00440.59750.01180.17570.7361-0.05110.735111.731295.319442.3143
92.4936-0.10640.11583.562-0.23582.9019-0.02740.0426-0.10580.4298-0.0345-0.2460.21230.17810.05970.48750.0337-0.03380.27780.13610.4253124.0156-22.391445.2066
102.99350.5135-1.09471.9659-0.12044.23120.7751-0.47610.13130.9024-0.53990.0344-1.33780.1839-0.21041.6126-0.23230.10590.9349-0.02590.993894.8831-19.5076-0.6517
110.79-0.27330.08831.94820.45580.963-0.2097-0.11570.1610.31410.2115-0.098-0.20860.0909-0.01840.53330.11090.0750.40150.11460.5046109.135338.531636.5799
126.49650.7280.17596.50651.69559.3735-0.06360.3549-0.75130.751-0.22280.69011.2567-0.95190.26130.5438-0.0570.18910.55950.04230.882185.7998.838522.0328
132.38720.22940.57671.03180.90361.9426-0.0901-0.3491-0.43850.45330.12950.54060.145-0.808-0.02870.59910.10220.32220.52380.18910.822886.776617.195338.619
141.0466-0.322-0.15230.94880.30821.3107-0.07630.11840.0140.14160.1370.0847-0.0575-0.0221-0.070.3150.05620.12480.30650.10610.4725104.701226.023821.7656
151.41970.01050.33044.66050.09584.3792-0.03920.31750.2361-0.1835-0.03120.286-0.4064-0.1170.05590.30430.01110.08120.35620.12360.4621105.867331.40399.0219
161.4041-0.34120.08333.56430.24381.6623-0.0708-0.0858-0.06390.47940.1208-0.05760.0204-0.0112-0.0320.30570.07550.08290.30810.12190.4007111.541313.711139.4234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 2 through 106 )
2X-RAY DIFFRACTION2chain 'C' and (resid 107 through 136 )
3X-RAY DIFFRACTION3chain 'C' and (resid 137 through 182 )
4X-RAY DIFFRACTION4chain 'C' and (resid 183 through 320 )
5X-RAY DIFFRACTION5chain 'C' and (resid 321 through 400 )
6X-RAY DIFFRACTION6chain 'C' and (resid 401 through 631 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 314 )
8X-RAY DIFFRACTION8chain 'D' and (resid 315 through 708 )
9X-RAY DIFFRACTION9chain 'A' and (resid 1 through 302 )
10X-RAY DIFFRACTION10chain 'A' and (resid 303 through 708 )
11X-RAY DIFFRACTION11chain 'B' and (resid 3 through 106 )
12X-RAY DIFFRACTION12chain 'B' and (resid 107 through 136 )
13X-RAY DIFFRACTION13chain 'B' and (resid 137 through 182 )
14X-RAY DIFFRACTION14chain 'B' and (resid 183 through 351 )
15X-RAY DIFFRACTION15chain 'B' and (resid 352 through 400 )
16X-RAY DIFFRACTION16chain 'B' and (resid 401 through 631 )

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