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)


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

  • 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.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Corrinoid iron-sulfur protein large subunitA [auth F]450Clostridium autoethanogenum DSM 10061Mutation(s): 0 
UniProt
Find proteins for A0A3M0S5D2 (Clostridium autoethanogenum)
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Go to UniProtKB:  A0A3M0S5D2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3M0S5D2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CO-methylating acetyl-CoA synthaseB [auth D],
D [auth A]
708Clostridium autoethanogenum DSM 10061Mutation(s): 0 
EC: 2.3.1.169
UniProt
Find proteins for A0A3M0S3T0 (Clostridium autoethanogenum)
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Go to UniProtKB:  A0A3M0S3T0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3M0S3T0
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Acetyl-CoA decarbonylase/synthase complex subunit deltaC [auth E]314Clostridium autoethanogenum DSM 10061Mutation(s): 0 
UniProt
Find proteins for F8TEQ6 (Clostridium autoethanogenum)
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Entity Groups  
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UniProt GroupF8TEQ6
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Carbon monoxide dehydrogenase/acetyl-CoA synthase beta subunitE [auth B],
F [auth C]
630Clostridium autoethanogenum DSM 10061Mutation(s): 0 
EC: 1.2.7.4
UniProt
Find proteins for A0A3M0S5E1 (Clostridium autoethanogenum)
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UniProt GroupA0A3M0S5E1
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B12 (Subject of Investigation/LOI)
Query on B12

Download Ideal Coordinates CCD File 
H [auth F]COBALAMIN
C62 H89 Co N13 O14 P
LKVIQTCSMMVGFU-DWSMJLPVSA-N
RQM (Subject of Investigation/LOI)
Query on RQM

Download Ideal Coordinates CCD File 
N [auth B],
P [auth C]
Fe(3)-Ni(1)-S(4) cluster
Fe4 Ni S4
QGLWBXDZIHZONR-UHFFFAOYSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
G [auth F],
I [auth D],
L [auth B],
M [auth B],
O [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
NI (Subject of Investigation/LOI)
Query on NI

Download Ideal Coordinates CCD File 
J [auth D],
K [auth D]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-02-12
    Changes: Data collection, Database references
  • Version 1.2: 2025-02-19
    Changes: Data collection
  • Version 1.3: 2025-07-09
    Changes: Data collection