Affinage

CDC40

Pre-mRNA-processing factor 17 · UniProt O60508

Length
579 aa
Mass
65.5 kDa
Annotated
2026-06-09
17 papers in source corpus 14 papers cited in narrative 14 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

CDC40/PRP17 is a WD-repeat spliceosomal protein that promotes the second catalytic step of pre-mRNA splicing and, through selective splicing of intron-containing transcripts, governs cell cycle progression (PMID:9524131, PMID:15133121). It joins the spliceosome late, at the pre-catalytic A1 complex after U4 dissociation, associates with U2, U5, and U6 snRNPs without being a core subunit of any single snRNP, and remains bound through post-splicing lariat-containing complexes (PMID:18691155); in its absence stalled spliceosomes fail to undergo the Prp16 helicase-triggered conformational switch required for the second step (PMID:18691155). CDC40 acts at the 3' splice site, where it genetically and physically cooperates with Prp8 and the second-step machinery, and where its N-terminal non-conserved region mediates interactions with Prp16, Prp18, and U5 snRNA (PMID:10628969, PMID:8722761). Its requirement is substrate-selective: it is preferentially needed for introns longer than 200 nt and is dispensable when the branch point lies within ~13 nt of the 3' splice site (PMID:15452114). Through this selectivity CDC40 controls mitosis and cell cycle entry by ensuring splicing of specific transcripts including ANC1, the alpha-tubulins TUB1/TUB3, and CDCA5, loss of which causes G2/M and G1/S defects, growth arrest, and apoptosis (PMID:15133121, PMID:12711678, PMID:39747150). In humans, biallelic loss-of-function mutations in PRP17 cause pontocerebellar hypoplasia with microcephaly, with neuron-specific apoptosis driven by disrupted splicing of short, high-GC introns, and the protein forms an isomerase-substrate interaction with PPIL1 whose catalytic activity is non-essential (PMID:33220177).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 1986 Medium

    Before its splicing role was known, CDC40 was placed genetically in a DNA-damage response, establishing an early functional handle on the gene's phenotype.

    Evidence Double-mutant epistasis and DNA-damage survival assays in yeast G1 stationary cells

    PMID:3523226

    Open questions at the time
    • Cannot distinguish a direct repair role from an indirect consequence of defective splicing of repair-pathway transcripts
    • No molecular mechanism linking CDC40 to RAD6/RAD50 defined
  2. 1996 High

    Mapping ts alleles localized the functional core to the N-terminal non-conserved region rather than the WD repeats, redefining which part of the protein mediates second-step interactions.

    Evidence Mutagenesis of 11 missense alleles, deletion analysis, and allele-specific genetic interactions in yeast

    PMID:8722761

    Open questions at the time
    • Structural basis of the N-terminal Prp16/Prp18/U5 interactions not resolved
    • Role of the WD repeats left undefined
  3. 1998 High

    Two studies established that the human ortholog acts specifically at step II of splicing and associates with the spliceosome late, demonstrating cross-species functional conservation.

    Evidence Immunodepletion/add-back of splicing extracts, spliceosome association assays, and yeast-human chimera complementation with co-IP of splicing intermediates

    PMID:9524131 PMID:9769104

    Open questions at the time
    • Precise biochemical contribution to step II catalysis not mechanistically defined
    • Timing relative to other late factors not yet resolved
  4. 2000 High

    Genetic suppression and synthetic lethality with PRP8 alleles, plus suppression of 3' splice site mutations, positioned CDC40 as a Prp8-interacting 3' splice site recognition factor.

    Evidence Epistasis/synthetic-lethality analysis and ACT1-CUP1 splicing reporter in yeast

    PMID:10628969

    Open questions at the time
    • Direct physical contact with Prp8 vs. allele-bridged genetic interaction not distinguished
    • Molecular nature of 3' splice site recognition by CDC40 unresolved
  5. 2001 Medium

    Linking the SRPK kinase Sky1p to CDC40 in 3' splice site fidelity introduced phosphoregulation into the second-step recognition pathway.

    Evidence Synthetic lethality screen and ACT1-CUP1 reporter assay in yeast

    PMID:11565750

    Open questions at the time
    • Direct phosphorylation target of Sky1p in this pathway not identified
    • Whether CDC40 itself is phosphorylated not established
  6. 2003 High

    Identifying TUB1/TUB3 as splicing targets connected CDC40's splicing defect to a concrete mitotic phenotype via reduced alpha-tubulin.

    Evidence In vitro splicing of TUB3 pre-mRNA, intronless gene replacement suppression, and transcript analysis in yeast

    PMID:12711678

    Open questions at the time
    • Multiple limiting targets implied since intronless TUB1 does not rescue temperature sensitivity
    • Other mitotic targets not enumerated
  7. 2004 High

    Two studies defined CDC40's substrate selectivity—an intron-length/branch-point dependence and a specific cell-cycle target (ANC1)—explaining why only certain transcripts require it.

    Evidence Splicing-sensitive microarrays with in vitro splicing of defined substrates, plus intron-deletion suppression and intron point-mutation analysis in yeast

    PMID:15133121 PMID:15452114

    Open questions at the time
    • Mechanism by which intron length/branch-point distance sets CDC40 dependency not defined
    • Full set of length-dependent endogenous targets not catalogued
  8. 2006 Medium

    A G1/S role and cyclin/metabolic crosstalk broadened CDC40's cell-cycle function beyond mitosis.

    Evidence cDNA overexpression suppressor screen, cell cycle arrest/release, and double-mutant construction in yeast

    PMID:17171376

    Open questions at the time
    • Suppressing cDNAs are intronless, so the mechanistic link between splicing and G1/S remains indirect
    • Whether glycolytic/translation suppression reflects a genuine pathway or bypass unclear
  9. 2008 High

    Defining the snRNP associations and assembly stage established that CDC40 enters at the A1 complex and is needed for the Prp16-triggered second-step conformational switch.

    Evidence Reciprocal co-IP of snRNAs with tagged Prp17, staged in vitro spliceosome assembly, and splicing kinetics in yeast

    PMID:18691155

    Open questions at the time
    • Structural details of how CDC40 enables the Prp16 switch not resolved
    • Order of recruitment relative to other second-step factors not fully mapped
  10. 2010 Medium

    C. elegans work showed the developmental roles of the ortholog (meiotic entry, sex determination) derive from its conserved splicing function rather than a novel activity.

    Evidence Genetic epistasis by RNAi in sensitized backgrounds and yeast complementation rescue

    PMID:20419786

    Open questions at the time
    • Specific spliced targets underlying germline phenotypes not identified
    • Direct vs. indirect action within GLD-1 pathway not dissected
  11. 2020 High

    Human genetics tied PRP17 to a Mendelian neurodevelopmental disease and revealed a PPIL1 isomerase-substrate interaction whose catalytic activity is dispensable.

    Evidence Patient mutation identification, embryonic-lethal mouse knockouts, knockin mice with neuronal apoptosis, genome-wide splicing analysis, and isomerase assay

    PMID:33220177

    Open questions at the time
    • Why neurons are selectively vulnerable not mechanistically resolved
    • Functional role of the non-catalytic PPIL1 interaction unclear
  12. 2025 Medium

    In human cancer cells CDC40 was shown to control CDCA5 expression via intron retention, extending its substrate-selective cell-cycle control to mammalian transcripts.

    Evidence siRNA knockdown with RNA-seq splicing analysis, CDCA5 Western blot, and co-IP/mass spectrometry in lung cancer cells

    PMID:39747150

    Open questions at the time
    • Whether CDCA5 retention fully accounts for the proliferation/apoptosis phenotype not established
    • Direct vs. indirect effect on the CDCA5 first intron not distinguished

Open questions

Synthesis pass · forward-looking unresolved questions
  • How CDC40's substrate selectivity (intron length, GC content, branch-point distance) is mechanistically encoded at the spliceosome, and how this selectivity drives tissue-specific outcomes such as neuronal survival, remains unresolved.
  • No structural model of CDC40 within the catalytic spliceosome
  • Mechanism translating splicing selectivity into cell-type-specific phenotypes unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 2 GO:0140098 catalytic activity, acting on RNA 2
Localization
GO:0005634 nucleus 1
Pathway
R-HSA-1640170 Cell Cycle 3 R-HSA-8953854 Metabolism of RNA 2
Partners
PPIL1PRP16PRP18PRP8SKY1SLU7
Complex memberships
spliceosome

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1998 Human PRP17 (hPRP17/CDC40) is required for the second catalytic step of pre-mRNA splicing; immunodepletion of hPRP16 from splicing extracts specifically blocks step II, and both hPrp16 and hPrp17 associate with the spliceosome late in the splicing pathway. Mutations at the 3' splice site that block step II do not prevent hPrp16/hPrp17 spliceosome association, placing their function prior to 3' splice site recognition. Immunodepletion from splicing extracts, recombinant protein add-back, spliceosome association assays The EMBO journal High 9524131
1998 A yeast-human chimera carrying the C-terminal two-thirds of hPRP17 (containing WD repeats) complements both the cell-cycle and splicing defects of a yeast prp17 mutant; yeast and chimeric Prp17 proteins co-precipitate the intron-exon 2 lariat intermediate and the intron lariat product, demonstrating spliceosome association and functional conservation. Complementation of yeast prp17 mutant, co-immunoprecipitation of splicing intermediates RNA (New York, N.Y.) High 9769104
2000 PRP8 alleles suppress both the temperature-sensitive growth phenotype and the splicing defect caused by absence of Prp17/Cdc40, and other PRP8 alleles show synthetic lethality with prp17 deletion; PRP8 mutations also suppress specific 3' splice site mutations in an ACT1-CUP1 reporter, placing Prp17 and Prp8 as interacting partners during the second catalytic step of splicing, with PRP17/CDC40 acting in 3' splice site recognition. Genetic suppression/synthetic lethality analysis, ACT1-CUP1 splicing reporter assay Genetics High 10628969
1996 Missense mutations in three temperature-sensitive prp17 alleles map to the N-terminal non-conserved region; the N-terminal region (not the WD-repeat C-terminus) is the functional domain required for interactions with Prp16, Prp18, and U5 snRNA; a mutually allele-specific interaction between Prp17 and snr7 (U5 snRNA) was identified. In vitro mutagenesis of WD repeats, deletion analysis, genetic synthetic lethality, allele-specific interaction mapping Genetics High 8722761
2001 The SRPK family kinase Sky1p genetically interacts with PRP17/SLU4 in 3' splice site recognition; deletion of SKY1 is synthetically lethal with all prp17 mutants tested and suppresses 3' AG mutations in ACT1-CUP1 splicing reporters, indicating that phosphorylation by Sky1p regulates 3' splice site fidelity in a pathway involving Prp17. Synthetic lethality screen, ACT1-CUP1 splicing reporter assay RNA (New York, N.Y.) Medium 11565750
2004 CDC40/PRP17 controls cell cycle progression specifically through splicing of the ANC1 gene; deletion of the ANC1 intron relieves the cell cycle arrest and temperature sensitivity of cdc40 mutants, and point mutations in specific residues of the ANC1 intron define sequences required for CDC40-dependent splicing. Intron deletion suppression of cdc40 phenotype, point mutation analysis of intron sequences Nucleic acids research High 15133121
2004 Genome-wide microarray analysis shows Prp17 is preferentially required for splicing of introns longer than 200 nt, and is dispensable when the distance between the branch point nucleotide and the 3' splice site is ≤13 nt; in vitro splicing with substrates of varying branch-point to 3' splice site distances confirmed differential Prp17 dependency. Splicing-sensitive DNA microarray, in vitro splicing assay with defined pre-mRNA substrates The Journal of biological chemistry High 15452114
2003 Prp17 (Cdc40) is required for efficient splicing of TUB1 and TUB3 (alpha-tubulin) pre-mRNAs; reduced alpha-tubulin protein levels underlie the benomyl sensitivity and G2/M arrest of prp17 mutants; genomic replacement with an intronless TUB1 gene relieves the benomyl sensitivity but not the temperature sensitivity, indicating multiple limiting targets for mitosis. In vitro splicing with TUB3 pre-mRNA in prp17 extracts, intronless gene replacement suppression, RT-PCR/transcript analysis Nucleic acids research High 12711678
2008 Prp17 interacts with U2, U5, and U6 snRNPs but is not a core component of any single snRNP; it joins the spliceosome at the pre-catalytic A1 complex (after U4 dissociation), prior to both catalytic steps, and remains associated in post-splicing complexes containing lariat intron; in prp17Δ extracts, stalled spliceosomes are compromised for the Prp16 helicase-triggered conformational switch required for the second step. Co-immunoprecipitation of snRNAs using epitope-tagged Prp17, in vitro spliceosome assembly and co-precipitation on actin pre-mRNA, in vitro splicing kinetics The Biochemical journal High 18691155
2010 C. elegans PRP-17 (ortholog of PRP17/CDC40) functions downstream of GLP-1 Notch signaling to promote meiotic entry largely via the GLD-1 pathway, and functions in female germline sex determination; PRP-17 can rescue temperature-sensitive lethality of yeast PRP17, confirming functional conservation and demonstrating that splicing per se (not a novel function) underlies these developmental roles. Genetic epistasis (RNAi in sensitized backgrounds), yeast complementation rescue Developmental dynamics Medium 20419786
2020 Biallelic loss-of-function mutations in PRP17 cause pontocerebellar hypoplasia with microcephaly (PCHM) in humans; loss of PRP17 disrupts splicing integrity, predominantly affecting short and high GC-content introns and genes involved in brain disorders; PPIL1 and PRP17 form an active isomerase-substrate interaction, but isomerase activity per se is not critical for function. Patient mutation identification, mouse knockouts (embryonic lethal), knockin mouse neuronal apoptosis, RNA splicing analysis Neuron High 33220177
2025 CDC40 knockdown in lung cancer cells induces intron retention in CDCA5 pre-mRNA (specifically retention of the first intron), leading to decreased CDCA5 protein expression; co-immunoprecipitation reveals spliceosome components as the main binding partners of CDC40; CDC40 knockdown causes cell cycle defects, growth inhibition, and apoptosis. siRNA knockdown, RNA-seq/splicing analysis, Western blot for CDCA5 protein, co-immunoprecipitation/mass spectrometry Scientific reports Medium 39747150
2006 CDC40/PRP17 has a role in the G1/S transition: cdc40 mutants show delayed G1/S and hypersensitivity to HU/MMS; deletion of G1 cyclin CLN2 enhances temperature sensitivity and G1/S delay in cdc40 cells; overexpression of cDNAs encoding chaperones, translation initiation factors, and glycolytic enzymes (none intron-containing) can suppress HU/MMS sensitivity and G1/S delay, suggesting crosstalk between splicing, translation, and glycolysis at cell cycle entry. cDNA overexpression suppressor screen, arrest/release cell cycle analysis, double mutant construction Current genetics Medium 17171376
1986 Epistasis analysis shows that rad6-1 is epistatic to cdc40-1 for sensitivity to UV and MMS, and rad50-1 is epistatic to cdc40-1 for MMS sensitivity in G1 stationary cells, placing CDC40 in the RAD6 DNA-repair pathway; cdc40-1 mutants are defective in UV-induced mutagenesis at the restrictive temperature. Double mutant epistasis analysis, survival assays after DNA damage Mutation research Medium 3523226

Source papers

Stage 0 corpus · 17 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1998 Human homologs of yeast prp16 and prp17 reveal conservation of the mechanism for catalytic step II of pre-mRNA splicing. The EMBO journal 64 9524131
2010 PRP-17 and the pre-mRNA splicing pathway are preferentially required for the proliferation versus meiotic development decision and germline sex determination in Caenorhabditis elegans. Developmental dynamics : an official publication of the American Association of Anatomists 63 20419786
2020 Mutations in Spliceosomal Genes PPIL1 and PRP17 Cause Neurodegenerative Pontocerebellar Hypoplasia with Microcephaly. Neuron 48 33220177
2000 Extensive genetic interactions between PRP8 and PRP17/CDC40, two yeast genes involved in pre-mRNA splicing and cell cycle progression. Genetics 40 10628969
1998 Identification and functional analysis of hPRP17, the human homologue of the PRP17/CDC40 yeast gene involved in splicing and cell cycle control. RNA (New York, N.Y.) 38 9769104
2004 The Saccharomyces cerevisiae gene CDC40/PRP17 controls cell cycle progression through splicing of the ANC1 gene. Nucleic acids research 37 15133121
2016 HBx-induced MiR-1269b in NF-κB dependent manner upregulates cell division cycle 40 homolog (CDC40) to promote proliferation and migration in hepatoma cells. Journal of translational medicine 34 27349221
1985 Cloning and mapping of CDC40, a Saccharomyces cerevisiae gene with a role in DNA repair. Current genetics 33 3916722
2001 Evidence for a role of Sky1p-mediated phosphorylation in 3' splice site recognition involving both Prp8 and Prp17/Slu4. RNA (New York, N.Y.) 26 11565750
2004 Genome-wide analysis of pre-mRNA splicing: intron features govern the requirement for the second-step factor, Prp17 in Saccharomyces cerevisiae and Schizosaccharomyces pombe. The Journal of biological chemistry 24 15452114
1996 Genetic studies of the PRP17 gene of Saccharomyces cerevisiae: a domain essential for function maps to a nonconserved region of the protein. Genetics 20 8722761
2003 Dependence of pre-mRNA introns on PRP17, a non-essential splicing factor: implications for efficient progression through cell cycle transitions. Nucleic acids research 19 12711678
2006 A role for the yeast cell cycle/splicing factor Cdc40 in the G1/S transition. Current genetics 18 17171376
2008 The splicing factor Prp17 interacts with the U2, U5 and U6 snRNPs and associates with the spliceosome pre- and post-catalysis. The Biochemical journal 17 18691155
1986 DNA-repair characterization of cdc40-1, a cell-cycle mutant of Saccharomyces cerevisiae. Mutation research 14 3523226
2020 MiR-422a in gastric cancer cells directly targets CDC40 and modulates cell proliferation. American journal of translational research 4 32913542
2025 CDC40 suppression induces CDCA5 splicing defects and anti-proliferative effects in lung cancer cells. Scientific reports 1 39747150

Missed literature

Know a paper Affinage missed for CDC40? Flag it for the maintainers and the community.

No submissions yet.