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Structure paper

TitleFunctional and structural characterization of F-ATPase with common ancestral core domains in stator ring.
Journal, issue, pagesProtein Sci, Vol. 34, Issue 11, Page e70345, Year 2025
Publish dateOct 24, 2025
AuthorsAya K Suzuki / Ryutaro Furukawa / Meghna Sobti / Simon H J Brown / Alastair G Stewart / Satoshi Akanuma / Hiroshi Ueno / Hiroyuki Noji /
PubMed AbstractExtant F-ATPases exhibit diverse rotational stepping behaviors-3-, 6-, or 9-step cycles-yet the evolutionary origin of these patterns remains unclear. Here, we used ancestral sequence reconstruction ...Extant F-ATPases exhibit diverse rotational stepping behaviors-3-, 6-, or 9-step cycles-yet the evolutionary origin of these patterns remains unclear. Here, we used ancestral sequence reconstruction to infer the catalytic β and non-catalytic α subunits of a putative ancestral F-ATPase. We then fused their functionally critical domains into the thermostable F from Bacillus PS3, yielding a stable chimeric enzyme. Cryo-EM revealed two distinct conformational states-binding and catalytic dwell states-separated by a ~34° rotation of the γ subunit, suggesting a fundamental six-step mechanism akin to that of extant six-stepping F-ATPases. Single-molecule rotation assays with ATP and the slowly hydrolyzed ATP analog ATPγS demonstrated that the chimeric motor is intrinsically a six-stepper, pausing at binding and catalytic dwell positions separated by 32.1°, although the binding dwell is significantly prolonged by an unknown mechanism. These findings indicate that F-ATPase was originally a six-stepper and diversified into 3-, 6- and 9-step forms in evolutionary adaptation. Based on these results, we discuss plausible features of the entire FF complex, along with potential physiological contexts in the last universal common ancestor and related lineages.
External linksProtein Sci / PubMed:41131942 / PubMed Central
MethodsEM (single particle)
Resolution2.46 - 2.77 Å
Structure data

49839

9nvl

EMDB-49839, PDB-9nvl:
ATPase Hybrid F1 with the ancestral core domains Binding Dwell
Method: EM (single particle) / Resolution: 2.46 Å

49840

9nvm

EMDB-49840, PDB-9nvm:
ATPase Hybrid F1 with the ancestral core domains Catalytic Dwell
Method: EM (single particle) / Resolution: 2.58 Å

EMDB-49841: ATPase hybrid F1 with the ancestral core domains Hexamer without stalk Binding dwell
Method: EM (single particle) / Resolution: 2.77 Å

EMDB-49842: ATPase hybrid F1 with the ancestral core domains Tetramer with stalk Binding Dwell
Method: EM (single particle) / Resolution: 2.46 Å

EMDB-49843: ATPase hybrid F1 with the ancestral core domains Tetramer no stalk Binding Dwell
Method: EM (single particle) / Resolution: 2.68 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-PO4:
PHOSPHATE ION

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Source
  • bacillus sp. ps3 (bacteria)
  • pseudomonas aeruginosa (bacteria)
KeywordsELECTRON TRANSPORT / single particle / Ancestral ATPase / Enerygy

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