9FZY | pdb_00009fzy

Structure of carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) in complex with corrinoid iron-sulfur protein (CoFeSP) from Clostridium autoethanogenum (composite structure, class 3A)

PDB DOI: https://doi.org/10.2210/pdb9FZY/pdb
EM Map EMD-50897: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Clostridium autoethanogenum DSM 10061
Mutation(s): No

Deposited: 2024-07-06 Released: 2025-02-05
Deposition Author(s): Yin, M.D., Lemaire, O.N., Wagner, T., Murphy, B.J.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.71 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Conformational dynamics of a multienzyme complex in anaerobic carbon fixation.

Yin, M.D., Lemaire, O.N., Rosas Jimenez, J.G., Belhamri, M., Shevchenko, A., Hummer, G., Wagner, T., Murphy, B.J.

(2025) Science 387: 498-504

PubMed: 39883773 Search on PubMed
DOI: https://doi.org/10.1126/science.adr9672
Primary Citation of Related Structures:
9FZY, 9FZZ, 9G00, 9G01, 9G02, 9G03, 9G7I

PubMed Abstract:
In the ancient microbial Wood-Ljungdahl pathway, carbon dioxide (CO ₂) 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 Clostridium autoethanogenum , characterizing the molecular choreography of the overall reaction, including electron transfer to the CODH for CO ₂ 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 ₂ fixation in anaerobic organisms.

Organizational Affiliation

Redox and Metalloprotein Research Group, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.

Macromolecule Content

Total Structure Weight: 377.35 kDa
Atom Count: 22,924
Modeled Residue Count: 3,009
Deposited Residue Count: 3,440
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Corrinoid iron-sulfur protein large subunit	A [auth F]	450	Clostridium autoethanogenum DSM 10061	Mutation(s): 0
UniProt
Find proteins for A0A3M0S5D2 (Clostridium autoethanogenum) Explore A0A3M0S5D2 Go to UniProtKB: A0A3M0S5D2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3M0S5D2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CO-methylating acetyl-CoA synthase	B [auth D], D [auth A]	708	Clostridium autoethanogenum DSM 10061	Mutation(s): 0 EC: 2.3.1.169
UniProt
Find proteins for A0A3M0S3T0 (Clostridium autoethanogenum) Explore A0A3M0S3T0 Go to UniProtKB: A0A3M0S3T0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3M0S3T0
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA decarbonylase/synthase complex subunit delta	C [auth E]	314	Clostridium autoethanogenum DSM 10061	Mutation(s): 0
UniProt
Find proteins for F8TEQ6 (Clostridium autoethanogenum) Explore F8TEQ6 Go to UniProtKB: F8TEQ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F8TEQ6
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase/acetyl-CoA synthase beta subunit	E [auth B], F [auth C]	630	Clostridium autoethanogenum DSM 10061	Mutation(s): 0 EC: 1.2.7.4
UniProt
Find proteins for A0A3M0S5E1 (Clostridium autoethanogenum) Explore A0A3M0S5E1 Go to UniProtKB: A0A3M0S5E1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3M0S5E1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B12 (Subject of Investigation/LOI) Query on B12 Download Ideal Coordinates CCD File SDF format, chain H [auth F] MOL2 format, chain H [auth F] mmCIF format, chain H [auth F]	H [auth F]	COBALAMIN C₆₂ H₈₉ Co N₁₃ O₁₄ P LKVIQTCSMMVGFU-DWSMJLPVSA-N		Interactions Focus chain H [auth F] Interactions & Density Focus chain H [auth F]
RQM (Subject of Investigation/LOI) Query on RQM Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain N [auth B]	N [auth B], P [auth C]	Fe(3)-Ni(1)-S(4) cluster Fe₄ Ni S₄ QGLWBXDZIHZONR-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain P [auth C] Interactions & Density Focus chain N [auth B] Focus chain P [auth C]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain I [auth D] SDF format, chain G [auth F] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain I [auth D] MOL2 format, chain G [auth F] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain I [auth D] mmCIF format, chain G [auth F]	G [auth F], I [auth D], L [auth B], M [auth B], O [auth C]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain G [auth F] Focus chain I [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Interactions & Density Focus chain G [auth F] Focus chain I [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C]
NI (Subject of Investigation/LOI) Query on NI Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain J [auth D] mmCIF format, chain K [auth D] mmCIF format, chain J [auth D]	J [auth D], K [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain J [auth D] Focus chain K [auth D] Interactions & Density Focus chain J [auth D] Focus chain K [auth D]