Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Ligand binding to a Ni-Fe cluster orchestrates conformational changes of the CO-dehydrogenase-acetyl-CoA synthase complex.
Journal, issue, pages	Nat Catal, Vol. 8, Issue 7, Page 657-667, Year 2025
Publish date	Jul 11, 2025
Authors	Jakob Ruickoldt / Julian Kreibich / Thomas Bick / Jae-Hun Jeoung / Benjamin R Duffus / Silke Leimkühler / Holger Dobbek / Petra Wendler /
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 ...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.
External links	Nat Catal / PubMed:40727002 / PubMed Central
Methods	EM (single particle)
Resolution	1.9 - 10.0 Å
Structure data	50588 9fnc EMDB-50588, PDB-9fnc: Half-closed CODH/ACS in the carbonylated state Method: EM (single particle) / Resolution: 2.21 Å 50598 9fnj EMDB-50598, PDB-9fnj: Half-closed CODH/ACS in the acetylated state Method: EM (single particle) / Resolution: 2.0 Å 50616 9fo4 EMDB-50616, PDB-9fo4: Half-closed CODH/ACS (Class 2) in the methylated state Method: EM (single particle) / Resolution: 2.47 Å 50626 9fop EMDB-50626, PDB-9fop: Half-closed CODH/ACS (Class 1) in the methylated state Method: EM (single particle) / Resolution: 2.33 Å 50631 9fox EMDB-50631, PDB-9fox: Half-closed CODH/ACS in the reduced state Method: EM (single particle) / Resolution: 2.31 Å 50674 9fr0 EMDB-50674, PDB-9fr0: Triangle state of ACS found in the as-isolated state Method: EM (single particle) / Resolution: 3.42 Å 50677 9fr1 EMDB-50677, PDB-9fr1: Half-closed CODH/ACS in the as-isolated state Method: EM (single particle) / Resolution: 2.2 Å EMDB-50729: Extended state of carbonylated CODH/ACS (3D flex consensus map) Method: EM (single particle) / Resolution: 10.0 Å 50754 9fu3 EMDB-50754, PDB-9fu3: Closed CODH/ACS in the methylated state Method: EM (single particle) / Resolution: 2.35 Å 50756 9fu4 EMDB-50756, PDB-9fu4: Wobbly CODH/ACS in the as isolated state Method: EM (single particle) / Resolution: 1.9 Å 50757 9fu7 EMDB-50757, PDB-9fu7: Wobbly CODH/ACS in the reduced state Method: EM (single particle) / Resolution: 2.04 Å 50758 9fu9 EMDB-50758, PDB-9fu9: Wobbly CODH/ACS in the methylated state Method: EM (single particle) / Resolution: 2.24 Å 50759 9fua EMDB-50759, PDB-9fua: Wobbly CODH/ACS in the acetlyated state Method: EM (single particle) / Resolution: 2.04 Å 50760 9fub EMDB-50760, PDB-9fub: Wobbly CODH/ACS in the carbonylated state Method: EM (single particle) / Resolution: 1.98 Å 50761 9fuc EMDB-50761, PDB-9fuc: Wobbly CODH/ACS in the presence of CoA Method: EM (single particle) / Resolution: 2.06 Å EMDB-50837: CODH/ACS in the loose extended state in the presence of CoA (3D flex consensus map) Method: EM (single particle) / Resolution: 10.0 Å
Chemicals	ChemComp-RQM: Fe(3)-Ni(1)-S(4) cluster ChemComp-SF4: IRON/SULFUR CLUSTER ChemComp-CMO: CARBON MONOXIDE ChemComp-NI: NICKEL (II) ION ChemComp-NA: Unknown entry ChemComp-HOH: WATER ChemComp-FES: FE2/S2 (INORGANIC) CLUSTER ChemComp-ACE: ACETYL GROUP ChemComp-74C: methyl radical
Source	carboxydothermus hydrogenoformans (bacteria) carboxydothermus hydrogenoformans z-2901 (bacteria)
Keywords	OXIDOREDUCTASE / CODH / ACS / CO2 fixation / reductive acetyl-CoA pathway / Wood-Ljungdahl pathway