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- PDB-9g03: Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (C... -

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Basic information

Entry
Database: PDB / ID: 9g03
TitleStructure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with ferredoxin (Clostridium autoethanogenum)
Components
  • CO-methylating acetyl-CoA synthase
  • Carbon monoxide dehydrogenase/acetyl-CoA synthase beta subunit
  • Ferredoxin
KeywordsOXIDOREDUCTASE / anaerobic CO2 fixation / acetyl-CoA synthesis / metalloenzyme / Wood-Ljungdahl pathway.
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 / electron transfer activity / metal ion binding / cytoplasm
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 / 7Fe ferredoxin / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily ...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 / 7Fe ferredoxin / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / : / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Fe(3)-Ni(1)-S(4) cluster / IRON/SULFUR CLUSTER / Ferredoxin / CO-methylating acetyl-CoA synthase
Similarity search - Component
Biological speciesClostridium autoethanogenum DSM 10061 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsYin, M.D. / Lemaire, O.N. / Wagner, T. / Murphy, B.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society 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 6, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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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/acetyl-CoA synthase beta subunit
C: Carbon monoxide dehydrogenase/acetyl-CoA synthase beta subunit
D: CO-methylating acetyl-CoA synthase
E: Ferredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,13112
Polymers295,5525
Non-polymers2,5797
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#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)
References: UniProt: F8TEQ9, CO-methylating acetyl-CoA synthase
#2: Protein Carbon monoxide dehydrogenase/acetyl-CoA synthase beta subunit


Mass: 67846.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Clostridium autoethanogenum DSM 10061 (bacteria)
References: anaerobic carbon monoxide dehydrogenase
#3: Protein Ferredoxin


Mass: 5877.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Clostridium autoethanogenum DSM 10061 (bacteria)
References: UniProt: A0A3M0T3C4
#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-RQM / Fe(3)-Ni(1)-S(4) cluster


Mass: 410.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4NiS4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Carbon monoxide dehydrogenase/acetyl-CoA synthase in complex with ferredoxin
Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Clostridium autoethanogenum DSM 10061 (bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 896132 / Symmetry type: POINT
RefinementResolution: 2.1→183.96 Å / Cor.coef. Fo:Fc: 0.898 / SU B: 3.855 / SU ML: 0.091 / ESU R: 0.128
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.33352 --
obs0.33352 482685 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 44.072 Å2
Refinement stepCycle: 1 / Total: 14176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.010.01214435
ELECTRON MICROSCOPYr_bond_other_d00.01614222
ELECTRON MICROSCOPYr_angle_refined_deg1.7961.63719595
ELECTRON MICROSCOPYr_angle_other_deg0.8571.57132863
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.57851885
ELECTRON MICROSCOPYr_dihedral_angle_2_deg1.2485214
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.696102563
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.1210.22340
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.0216374
ELECTRON MICROSCOPYr_gen_planes_other0.0020.022790
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it1.7334.2287555
ELECTRON MICROSCOPYr_mcbond_other1.7334.2287555
ELECTRON MICROSCOPYr_mcangle_it3.0297.5959435
ELECTRON MICROSCOPYr_mcangle_other3.0297.5969436
ELECTRON MICROSCOPYr_scbond_it2.2164.6246880
ELECTRON MICROSCOPYr_scbond_other2.2144.6066857
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other3.9038.33310065
ELECTRON MICROSCOPYr_long_range_B_refined7.68650.1162783
ELECTRON MICROSCOPYr_long_range_B_other7.68750.162774
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.999 35735 -
obs--100 %

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