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

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Basic information

Entry
Database: PDB / ID: 9fzz
TitleStructure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with corrinoid iron-sulfur protein (CoFeSP) from Clostridium autoethanogenum (composite structure, class 3B)
Components
  • Acetyl-CoA decarbonylase/synthase complex subunit delta
  • CO-methylating acetyl-CoA synthase
  • Carbon monoxide dehydrogenase/acetyl-CoA synthase beta subunit
  • Corrinoid iron-sulfur protein large subunit
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 / metal ion binding
Similarity search - Function
CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel / : / CO dehydrogenase/acetyl-CoA synthase delta subunit / 4Fe-4S domain / Putative Fe-S cluster / 4Fe-4S domain profile. / 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 delta subunit, TIM barrel / : / CO dehydrogenase/acetyl-CoA synthase delta subunit / 4Fe-4S domain / Putative Fe-S cluster / 4Fe-4S domain profile. / 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 / Dihydropteroate synthase-like / Prismane-like superfamily
Similarity search - Domain/homology
COBALAMIN / NICKEL (II) ION / Fe(3)-Ni(1)-S(4) cluster / IRON/SULFUR CLUSTER / Acetyl-CoA decarbonylase/synthase complex subunit delta / Corrinoid iron-sulfur protein large subunit / CO-methylating acetyl-CoA synthase
Similarity search - Component
Biological speciesClostridium autoethanogenum DSM 10061 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 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 1.0Feb 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: 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
Revision 1.2Feb 19, 2025Group: Data collection / Category: em_admin / Item: _em_admin.last_update
Revision 1.3Jul 9, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: CO-methylating acetyl-CoA synthase
E: Acetyl-CoA decarbonylase/synthase complex subunit delta
A: CO-methylating acetyl-CoA synthase
B: Carbon monoxide dehydrogenase/acetyl-CoA synthase beta subunit
C: Carbon monoxide dehydrogenase/acetyl-CoA synthase beta subunit
F: Corrinoid iron-sulfur protein large subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)377,35116
Polymers373,3256
Non-polymers4,02710
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

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Protein , 4 types, 6 molecules DAEBCF

#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 Acetyl-CoA decarbonylase/synthase complex subunit delta / Corrinoid iron-sulfur protein small subunit / Corrinoid/iron-sulfur protein small subunit


Mass: 34037.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Clostridium autoethanogenum DSM 10061 (bacteria)
References: UniProt: F8TEQ6
#3: 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
#4: Protein Corrinoid iron-sulfur protein large subunit / Corrinoid/iron-sulfur protein large subunit


Mass: 49612.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Clostridium autoethanogenum DSM 10061 (bacteria)
References: UniProt: F8TEQ7

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Non-polymers , 4 types, 10 molecules

#5: 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
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#7: 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
#8: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION

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Details

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 corrinoid/iron-sulfur protein
Type: COMPLEX / Entity ID: #1-#4 / 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

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 649146 / Symmetry type: POINT
RefinementResolution: 2.65→2.65 Å / Cor.coef. Fo:Fc: 0.854 / SU B: 3.026 / SU ML: 0.077 / ESU R: 0.125
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.40794 --
obs0.40794 1005963 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 81.211 Å2
Refinement stepCycle: 1 / Total: 22924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0110.01223352
ELECTRON MICROSCOPYr_bond_other_d00.01622895
ELECTRON MICROSCOPYr_angle_refined_deg1.7281.64631671
ELECTRON MICROSCOPYr_angle_other_deg0.8031.57552938
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.36753003
ELECTRON MICROSCOPYr_dihedral_angle_2_deg1.2845315
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.418104177
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.1340.23706
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.0226517
ELECTRON MICROSCOPYr_gen_planes_other0.0020.024633
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_it2.0357.9212030
ELECTRON MICROSCOPYr_mcbond_other2.0357.9212030
ELECTRON MICROSCOPYr_mcangle_it3.51914.23415027
ELECTRON MICROSCOPYr_mcangle_other3.51914.23515028
ELECTRON MICROSCOPYr_scbond_it2.338.5211322
ELECTRON MICROSCOPYr_scbond_other2.338.52111323
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other4.13415.56816573
ELECTRON MICROSCOPYr_long_range_B_refined8.7193.2799200
ELECTRON MICROSCOPYr_long_range_B_other8.7193.2799201
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.279 74532 -
obs--100 %

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