Affinage

ATPAF1

ATP synthase mitochondrial F1 complex assembly factor 1 · UniProt Q5TC12

Length
328 aa
Mass
36.4 kDa
Annotated
2026-06-09
12 papers in source corpus 9 papers cited in narrative 9 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

ATPAF1 (Atp11p) is a mitochondrial matrix molecular chaperone that mediates a late step in assembly of the F1 catalytic sector of the mitochondrial ATP synthase (PMID:1532796, PMID:12206899). It binds selectively and physically to unassembled F1-ATPase beta-subunits, engaging residues Gly-114–Leu-318 of the beta-subunit nucleotide-binding domain — the same surface that contacts alpha-subunits in the mature enzyme — such that incoming alpha-subunits displace ATPAF1 to drive formation of the alpha3beta3 hexamer; in its absence alpha and beta subunits accumulate as inactive aggregates (PMID:1532796, PMID:10681564). The chaperone activity operates through a defined hydrophobic surface that shields aggregation-prone subunits, and ATPAF1 can hold a generic unfolding substrate (insulin B chain) as well as its natural beta-subunit client in vitro (PMID:11522798, PMID:12829692). The functional core of the protein maps to residues Phe-120–Asn-174, with the N-terminal targeting sequence and disordered N-terminus dispensable for activity (PMID:8617760, PMID:12829692). This chaperone function is structurally and functionally conserved from yeast through Drosophila to human, as human ATPAF1 complements the yeast mutant (PMID:10386611, PMID:11410595).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 1992 High

    Established that a dedicated factor, not just the structural subunits, is required for F1-ATPase biogenesis by showing its loss leaves alpha/beta subunits as inactive aggregates.

    Evidence Cloning, in vitro mitochondrial import, immunochemistry, and affinity pulldown of biotinylated Atp11p in S. cerevisiae

    PMID:1532796

    Open questions at the time
    • Did not resolve which subunit is the direct binding partner
    • Mechanism of aggregation prevention not defined
  2. 1995 Medium

    Showed the mature protein alone, without its targeting presequence, is sufficient for assembly function, separating import from chaperone activity.

    Evidence Bacterial expression of mature Atp11p and yeast complementation

    PMID:7771799

    Open questions at the time
    • Single lab
    • Did not map the functional core within the mature protein
  3. 1996 High

    Defined the functional architecture, mapping an active domain (Phe-120–Asn-174) and showing overall fold rather than a localized catalytic site is required.

    Evidence atp11 mutant sequencing, limited proteolysis with Edman analysis, deletion mutagenesis, yeast assays

    PMID:8617760

    Open questions at the time
    • No atomic structure of the active domain
    • Did not show how the domain engages substrate
  4. 1999 Medium

    Demonstrated functional conservation in metazoa, with a Drosophila homolog rescuing the yeast mutant and binding the yeast beta-subunit.

    Evidence Yeast complementation and two-hybrid with D. yakuba homolog

    PMID:10386611

    Open questions at the time
    • Cross-species; native Drosophila role not tested
    • Single lab
  5. 2000 High

    Identified the beta-subunit as the specific client and mapped the binding interface to a region that overlaps the alpha-subunit contact, suggesting subunit exchange drives assembly.

    Evidence Avidin-Sepharose pulldown and yeast two-hybrid with beta-subunit fragments

    PMID:10681564

    Open questions at the time
    • Exchange-during-assembly model not directly demonstrated
    • Stoichiometry of the complex unresolved
  6. 2001 High

    Defined ATPAF1 mechanistically as a hydrophobic-surface chaperone that prevents beta-subunit aggregation, with the surface required for activity.

    Evidence In vitro insulin B-chain and beta-subunit aggregation assays, bis-ANS and tryptophan fluorescence probing

    PMID:11522798

    Open questions at the time
    • Atomic identity of the hydrophobic surface residues not resolved
    • Does not show release/handoff step kinetics
  7. 2001 High

    Confirmed human ATPAF1 is a bona fide conserved assembly chaperone by functional complementation of yeast and characterized the human gene.

    Evidence cDNA isolation, yeast complementation, chromosomal mapping

    PMID:11410595

    Open questions at the time
    • No disease link established in this study
    • Human protein not assayed biochemically here
  8. 2003 High

    Localized chaperone activity to an ordered core, showing the disordered N-terminal region is dispensable and the active protein is amenable to structural study.

    Evidence Recombinant N-terminal truncation, in vitro chaperone assays, 15N-1H HSQC NMR

    PMID:12829692

    Open questions at the time
    • Full solution/atomic structure not solved
    • Substrate-bound complex not characterized

Open questions

Synthesis pass · forward-looking unresolved questions
  • How ATPAF1 hands off the beta-subunit to nascent alpha3beta3 and whether ATPAF1 dysfunction causes human disease remain unresolved.
  • No structure of the ATPAF1–beta-subunit complex
  • No human disease-causing mutation characterized in the corpus
  • Order of subunit recruitment during assembly not directly observed

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0044183 protein folding chaperone 4 GO:0098772 molecular function regulator activity 3
Localization
GO:0005739 mitochondrion 2
Pathway
R-HSA-1852241 Organelle biogenesis and maintenance 2
Partners
ATP5F1B

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1992 ATP11 (Atp11p) encodes a 37 kDa mitochondrial protein in S. cerevisiae; loss-of-function mutations cause alpha and beta subunits of F1-ATPase to accumulate as inactive aggregates, indicating a required role in a late step of F1 assembly. In vitro import assays and immunochemical evidence confirmed mitochondrial localization. Affinity-purified biotinylated Atp11p co-purified with alpha and beta subunits of F1-ATPase, indicating physical association. Cloning/sequencing, in vitro mitochondrial import assay, immunochemistry, affinity chromatography with biotinylated fusion protein, genetic complementation The Journal of biological chemistry High 1532796
1995 Recombinant mature Atp11p produced in bacteria retains biological activity as confirmed by yeast complementation assays, establishing that the N-terminal targeting sequence is dispensable for function and that the mature protein alone is sufficient for F1-ATPase assembly activity. Bacterial overexpression, protein purification, yeast complementation assay Archives of biochemistry and biophysics Medium 7771799
1996 The active domain of Atp11p was mapped to residues Phe-120 through Asn-174 by limited proteolysis and deletion mutagenesis. The N-terminal 39 residues constitute the mitochondrial targeting domain. Nonsense mutations throughout the mature protein sequence cause loss of function, indicating that overall protein structure (not a localized catalytic active site) is required for activity. Flanking domains (Glu-40–Ser-109 and Arg-183–Asn-318) are important for protein stability inside mitochondria. Cloning/sequencing of atp11 mutants, Edman sequence analysis of proteolytic fragments, deletion mutagenesis, yeast functional assays The Journal of biological chemistry High 8617760
2000 Atp11p binds selectively to the beta-subunit of F1-ATPase. Biotinylated Atp11p pulled down the F1 beta-subunit from yeast mitochondrial extracts. Yeast two-hybrid analysis mapped the Atp11p-binding region to residues Gly-114–Leu-318 of the beta-subunit nucleotide-binding domain — a region that contacts alpha-subunits in the assembled enzyme, suggesting alpha-subunits may exchange for Atp11p during F1 assembly. Avidin-Sepharose affinity pulldown of biotinylated Atp11p from mitochondrial extracts, yeast two-hybrid screen with beta-subunit fragments The Journal of biological chemistry High 10681564
1999 A Drosophila homolog of Atp11p (from D. yakuba gene 2A5) complements the respiratory-deficient phenotype of yeast atp11::HIS3 deletion mutants and interacts with the S. cerevisiae F1 beta-subunit in the yeast two-hybrid assay, establishing functional conservation of Atp11p chaperone activity in higher eukaryotes. Yeast complementation of atp11 deletion strain, yeast two-hybrid assay FEBS letters Medium 10386611
2001 Atp11p acts as a molecular chaperone by preventing unassembled F1-ATPase beta-subunits from aggregating in the mitochondrial matrix. Its chaperone activity is mediated by hydrophobic interactions: a hydrophobic surface identified by bis-ANS fluorescence probe binding accommodates up to three bis-ANS molecules cooperatively, and binding of even a single bis-ANS molecule virtually eliminates chaperone activity. Atp11p also protects the insulin B chain from aggregating in vitro (surrogate chaperone substrate). In vitro insulin B-chain aggregation assay, bis-ANS fluorescence probe binding, tryptophan fluorescence quenching, chaperone activity assays The Journal of biological chemistry High 11522798
2001 Human ATP11 (ATPAF1) and ATP12 proteins functionally complement their yeast counterparts, establishing that human Atp11p is a conserved assembly factor (chaperone) for the F1-ATPase in human mitochondria. The human ATP11 gene spans 24 kb in 9 exons and maps to chromosomal locus 1p32.3-p33. cDNA isolation, functional complementation of yeast mutants, chromosomal mapping The Journal of biological chemistry High 11410595
2002 Atp11p and Atp12p are molecular chaperones specifically required for assembly of the alpha and beta subunits of the mitochondrial F1-ATPase oligomer (alpha3beta3gamma-delta-epsilon); without them, alpha and beta subunits form inactive aggregates. This chaperone function is conserved between yeast and human mitochondria. Genetic and biochemical characterization in S. cerevisiae and human cells (review consolidating prior experimental evidence) Biochimica et biophysica acta High 12206899
2003 A truncated recombinant Atp11p lacking 67 N-terminal residues (Atp11pTRNC) retains full molecular chaperone activity in vitro against both reduced insulin (surrogate substrate) and the natural substrate F1 beta-subunit. Preliminary 15N-1H HSQC NMR spectra show the truncated protein is well-ordered, indicating the disordered N-terminal region is dispensable for chaperone function. Recombinant protein truncation, in vitro chaperone assay (insulin aggregation, F1 beta-subunit), 15N-1H HSQC NMR spectroscopy The Journal of biological chemistry High 12829692

Source papers

Stage 0 corpus · 12 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2001 Atp11p and Atp12p are assembly factors for the F(1)-ATPase in human mitochondria. The Journal of biological chemistry 80 11410595
2002 Atp11p and Atp12p are chaperones for F(1)-ATPase biogenesis in mitochondria. Biochimica et biophysica acta 51 12206899
1992 Characterization of ATP11 and detection of the encoded protein in mitochondria of Saccharomyces cerevisiae. The Journal of biological chemistry 50 1532796
2000 The assembly factor Atp11p binds to the beta-subunit of the mitochondrial F(1)-ATPase. The Journal of biological chemistry 42 10681564
2001 An accessible hydrophobic surface is a key element of the molecular chaperone action of Atp11p. The Journal of biological chemistry 33 11522798
2011 Identification of ATPAF1 as a novel candidate gene for asthma in children. The Journal of allergy and clinical immunology 24 21696813
1996 Identification of functional domains in Atp11p. Protein required for assembly of the mitochondrial F1-ATPase in yeast. The Journal of biological chemistry 21 8617760
1995 Bacterial production and characterization of ATP11, a yeast protein required for mitochondrial F1-ATPase assembly. Archives of biochemistry and biophysics 13 7771799
1999 The Drosophila gene 2A5 complements the defect in mitochondrial F1-ATPase assembly in yeast lacking the molecular chaperone Atp11p. FEBS letters 11 10386611
2003 A purified subfragment of yeast Atp11p retains full molecular chaperone activity. The Journal of biological chemistry 7 12829692
2003 Differential expression of ATPAF1 and ATPAF2 genes encoding F(1)-ATPase assembly proteins in mouse tissues. FEBS letters 7 12965202
2023 LINC00115 promotes gastric cancer partly by the miR-212-5p/ATPAF1 axis. Anais da Academia Brasileira de Ciencias 1 38088732

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