9FNJ | pdb_00009fnj

Half-closed CODH/ACS in the acetylated state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Ligand binding to a Ni-Fe cluster orchestrates conformational changes of the CO-dehydrogenase-acetyl-CoA synthase complex.

Ruickoldt, J.Kreibich, J.Bick, T.Jeoung, J.H.Duffus, B.R.Leimkuhler, S.Dobbek, H.Wendler, P.

(2025) Nat Catal 8: 657-667

  • DOI: https://doi.org/10.1038/s41929-025-01365-y
  • Primary Citation of Related Structures:  
    9FNC, 9FNJ, 9FO4, 9FOP, 9FOX, 9FR0, 9FR1, 9FU3, 9FU4, 9FU7, 9FU9, 9FUA, 9FUB, 9FUC

  • PubMed Abstract: 

    Catalytic metal clusters play critical roles in important enzymatic pathways such as carbon fixation and energy conservation. However, how ligand binding to the active-site metal regulates conformational changes critical for enzyme function is often not well understood. One carbon fixation pathway that relies heavily on metalloenzymes is the reductive acetyl-coenzyme A (acetyl-CoA) pathway. In this study, we investigated the catalysis of the last step of the reductive acetyl-CoA pathway by the CO-dehydrogenase (CODH)-acetyl-CoA synthase (ACS) complex from Carboxydothermus hydrogenoformans , focusing on how ligand binding to the nickel atom in the active site affects the conformational equilibrium of the enzyme. We captured six intermediate states of the enzyme by cryo-electron microscopy, with resolutions of 2.5-1.9 Å, and visualized reaction products bound to cluster A (an Ni,Ni-[4Fe4S] cluster) and identified several previously uncharacterized conformational states of CODH-ACS. The structures demonstrate how substrate binding controls conformational changes in the ACS subunit to prepare for the next catalytic step.


  • Organizational Affiliation
    • Department of Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CO-dehydrogenase
A, B
669Carboxydothermus hydrogenoformansMutation(s): 0 
EC: 1.2.7.4
UniProt
Find proteins for P27989 (Moorella thermoacetica)
Explore P27989 
Go to UniProtKB:  P27989
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27989
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CO-methylating acetyl-CoA synthase
C, D
730Carboxydothermus hydrogenoformansMutation(s): 0 
EC: 2.3.1.169
UniProt
Find proteins for P27988 (Moorella thermoacetica)
Explore P27988 
Go to UniProtKB:  P27988
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27988
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RQM (Subject of Investigation/LOI)
Query on RQM

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
Fe(3)-Ni(1)-S(4) cluster
Fe4 Ni S4
QGLWBXDZIHZONR-UHFFFAOYSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B],
S [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
NI (Subject of Investigation/LOI)
Query on NI

Download Ideal Coordinates CCD File 
R [auth C],
T [auth C]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
ACE (Subject of Investigation/LOI)
Query on ACE

Download Ideal Coordinates CCD File 
V [auth C]ACETYL GROUP
C2 H4 O
IKHGUXGNUITLKF-UHFFFAOYSA-N
CMO (Subject of Investigation/LOI)
Query on CMO

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
N [auth B]
O [auth B]
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
W [auth C],
X [auth C],
Y [auth D]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
U [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyEXC 2008/1 390540038

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-09-17
    Changes: Data collection, Database references