9FO4

Half-closed CODH/ACS (Class 2) in the methylated state

Summary for 9FO4

• Entry DOI: 10.2210/pdb9fo4/pdb
• EMDB information: 50616
• Descriptor: CO-dehydrogenase, CO-methylating acetyl-CoA synthase, Fe(3)-Ni(1)-S(4) cluster, ... (8 entities in total)
• Functional Keywords: codh, acs, co2 fixation, reductive acetyl-coa pathway, wood-ljungdahl pathway, oxidoreductase
• Biological source: Carboxydothermus hydrogenoformans; More
• Total number of polymer chains: 4
• Total formula weight: 313300.83

Authors

Ruickoldt, J.,Wendler, P.,Dobbek, H. (deposition date: 2024-06-11, release date: 2025-06-25, Last modification date: 2025-09-17)

Primary citation

Ruickoldt, J.,Kreibich, J.,Bick, T.,Jeoung, J.H.,Duffus, B.R.,Leimkuhler, S.,Dobbek, H.,Wendler, P.
Ligand binding to a Ni-Fe cluster orchestrates conformational changes of the CO-dehydrogenase-acetyl-CoA synthase complex.
Nat Catal, 8:657-667, 2025

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 , 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.

PubMed: 40727002
DOI: 10.1038/s41929-025-01365-y

Experimental method

ELECTRON MICROSCOPY (2.47 Å)