Affinage

CDC40

Pre-mRNA-processing factor 17 · UniProt O60508

Round 2 corrected
Length
579 aa
Mass
65.5 kDa
Annotated
2026-04-28
47 papers in source corpus 15 papers cited in narrative 16 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

CDC40 (PRP17) is a WD-repeat spliceosomal protein that functions specifically in the second catalytic step of pre-mRNA splicing, joining the spliceosome at the pre-catalytic A1 complex after U4 dissociation and facilitating the Prp16 helicase-driven conformational switch required for 3' splice site recognition (PMID:9524131, PMID:18691155). It associates with U2, U5, and U6 snRNPs and cooperates genetically with PRP8, PRP16, PRP18, and U5 snRNA during exon ligation, with preferential requirement for introns longer than 200 nt or with extended branch-point-to-3' splice site distances (PMID:10628969, PMID:15452114). CDC40 controls cell cycle progression at G1/S and G2/M by enabling efficient splicing of a subset of intron-containing cell cycle regulators including alpha-tubulin genes (TUB1/TUB3) and ANC1, and in human cells its loss causes CDCA5 intron retention and growth arrest (PMID:12711678, PMID:15133121, PMID:39747150). Biallelic loss-of-function mutations in CDC40 cause autosomal-recessive pontocerebellar hypoplasia with microcephaly in humans (PMID:33220177).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 1985 Medium

    Initial characterization of CDC40 in yeast revealed it as a cell-cycle gene with an unexpected role in DNA damage tolerance, linking it to the RAD6 repair pathway, though the molecular function was unknown.

    Evidence MMS/UV sensitivity assays of cdc40 temperature-sensitive mutants and epistasis analysis with rad6 and rad50 in S. cerevisiae

    PMID:3523226 PMID:3916722

    Open questions at the time
    • DNA repair phenotype likely indirect via splicing of repair gene transcripts — not resolved at this stage
    • No biochemical activity identified
  2. 1996 Medium

    Domain mapping established that the N-terminal region of PRP17, rather than its WD repeats, mediates functional interactions with other second-step splicing factors (PRP16, PRP18) and U5 snRNA, positioning PRP17 within the catalytic core of the spliceosome.

    Evidence Temperature-sensitive missense mutagenesis, synthetic lethality screens, and allele-specific interactions with snr7 in yeast

    PMID:8722761

    Open questions at the time
    • Physical basis of N-terminal domain interactions unresolved
    • No structural information for PRP17 in spliceosome context
  3. 1998 High

    Biochemical reconstitution demonstrated that CDC40/PRP17 is specifically required for the second catalytic step of pre-mRNA splicing, resolving the molecular basis of its spliceosome function and showing conservation from yeast to human.

    Evidence Immunodepletion of hPRP17 from HeLa splicing extracts blocks step II, rescued by recombinant protein; cross-species complementation of yeast prp17 mutant by human C-terminal WD-repeat domain

    PMID:9524131 PMID:9769104

    Open questions at the time
    • Mechanism of step II promotion not yet distinguished from structural scaffolding versus catalytic roles
    • Spliceosome entry point unknown
  4. 2000 High

    Extensive bidirectional genetic interactions with PRP8 placed PRP17 at the 3' splice site recognition stage of step II, establishing that these two factors collaborate during exon ligation.

    Evidence Genetic suppressor analysis showing PRP8 mutations suppress prp17Δ splicing defects and 3'SS mutations; reciprocal synthetic lethality using ACT1-CUP1 splicing reporter

    PMID:10628969

    Open questions at the time
    • Direct physical interaction between PRP8 and PRP17 not demonstrated
    • Structural basis of functional cooperation unknown
  5. 2003 High

    The long-standing cell cycle phenotype of cdc40 mutants was mechanistically explained: PRP17 controls G2/M progression by splicing alpha-tubulin pre-mRNAs, and cell cycle control of ANC1 splicing explains additional arrest phenotypes, demonstrating that a specific spliceosome factor governs cell division through differential intron processing.

    Evidence Intronless TUB1 gene replacement rescues benomyl sensitivity; ANC1 intron deletion rescues G2/M arrest and temperature sensitivity of cdc40 mutants; point mutation analysis of intron sequences

    PMID:12711678 PMID:15133121

    Open questions at the time
    • Full inventory of CDC40-dependent introns in yeast not established
    • Why these particular introns require PRP17 while others do not — cis-element rules incomplete
  6. 2004 High

    Genome-wide splicing microarray analysis revealed that PRP17 is preferentially required for introns >200 nt or with long branch-point-to-3'SS distances, establishing the intron-architecture determinants of PRP17 dependency.

    Evidence Splicing-sensitive microarrays in yeast prp17Δ, validated by in vitro splicing with defined substrates; comparative genetics in S. pombe where short introns dominate and Prp17 is non-essential

    PMID:15452114

    Open questions at the time
    • Molecular basis of distance-dependent PRP17 requirement unknown
    • Whether these rules fully apply to mammalian CDC40 not tested
  7. 2008 High

    Biochemical dissection defined the spliceosome entry point and mechanistic role: PRP17 joins at the A1 complex (post-U4 release), associates with U2/U5/U6 snRNPs, and is required for the Prp16-triggered conformational switch that enables step II catalysis.

    Evidence Co-immunoprecipitation of snRNAs with epitope-tagged Prp17, in vitro spliceosome assembly and stalling in prp17Δ extracts

    PMID:18691155

    Open questions at the time
    • Whether PRP17 directly contacts RNA or acts solely through protein-protein interactions unresolved
    • Structural position within C*/P complex not determined
  8. 2020 High

    Human genetic studies established that biallelic CDC40 loss-of-function causes pontocerebellar hypoplasia with microcephaly, revealing an essential neurodevelopmental role, with splicing defects predominantly affecting short, high-GC-content introns in brain-disorder genes — a substrate preference distinct from the yeast long-intron rule.

    Evidence Patient mutation identification, embryonic-lethal mouse knockout, knockin patient-mutation mice showing neuron-specific apoptosis, transcriptome-wide splicing analysis

    PMID:33220177

    Open questions at the time
    • Discrepancy between yeast (long introns affected) and human (short high-GC introns affected) substrate rules not reconciled
    • Neuron-specific vulnerability mechanism unclear
    • PPIL1–PRP17 interaction demonstrated but isomerase activity dispensable — functional role of interaction unknown
  9. 2025 Medium

    In human cancer cells, CDC40 depletion was shown to cause intron retention in CDCA5, linking spliceosome function to a specific cell-cycle regulator and identifying the CDC40 interactome as predominantly spliceosomal in human cells.

    Evidence siRNA knockdown in lung cancer lines, RNA-seq with RT-PCR validation of CDCA5 intron 1 retention, co-IP/mass spectrometry

    PMID:39747150

    Open questions at the time
    • CDCA5 intron retention as the primary cause of growth arrest versus broader splicing disruption not fully distinguished
    • Single study, not independently replicated

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key unresolved questions include the structural basis of CDC40/PRP17 action within the human spliceosome, the molecular rules governing which introns require CDC40 in mammalian cells, and the mechanistic basis of neuron-specific vulnerability to CDC40 loss.
  • No high-resolution structure of PRP17 within human C*/P spliceosome complex
  • Cis-element determinants of CDC40 dependency in mammalian introns undefined
  • No mechanistic explanation for tissue-specific (neuronal) sensitivity

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 3
Localization
GO:0005634 nucleus 3
Pathway
R-HSA-8953854 Metabolism of RNA 6 R-HSA-1640170 Cell Cycle 3
Partners
PPIL1PRP16PRP18PRP8SKY1
Complex memberships
Spliceosome (catalytic step II complex)

Evidence

Reading pass · 16 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1998 Human PRP17 (hPRP17/CDC40) is required specifically for the second catalytic step of pre-mRNA splicing. Immunodepletion of hPRP17 from splicing extracts blocks step II, which is rescued by recombinant hPRP17. Both hPRP16 and hPRP17 associate with the spliceosome late in the splicing pathway, at a stage prior to 3' splice site recognition. Immunodepletion from splicing extracts, rescue with recombinant protein, spliceosome association assays The EMBO journal High 9524131
1998 hPRP17 (CDC40 human homolog) contains WD repeats and its C-terminal two-thirds (including WD repeats) are sufficient to complement both cell cycle and splicing defects of a yeast prp17 mutant. The yeast and chimeric proteins co-precipitate the intron-exon 2 lariat intermediate and the intron lariat product, demonstrating spliceosome association during catalysis. Complementation of yeast prp17 mutant, co-immunoprecipitation of splicing intermediates RNA (New York, N.Y.) High 9769104
1985 CDC40 (yeast) has a role in DNA repair; cdc40 mutants are extremely sensitive to methyl methanesulfonate (MMS) at the restrictive temperature, suggesting the CDC40 gene product protects or holds together DNA during early stages of repair. The CDC40 gene was cloned and mapped to chromosome IV of S. cerevisiae. MMS sensitivity assay of cdc40 temperature-sensitive mutants, gene cloning and genetic mapping Current genetics Medium 3916722
1986 Epistasis analysis shows that rad6-1 is epistatic to cdc40-1 for UV and MMS sensitivity, placing CDC40 in the RAD6 DNA repair pathway. rad50-1 is epistatic to cdc40-1 for MMS sensitivity in G1 but not in logarithmic cultures. cdc40-1 mutants are defective in UV-induced mutagenesis at the restrictive temperature. Double-mutant epistasis analysis, UV/MMS survival assays Mutation research Medium 3523226
1996 Temperature-sensitive missense mutations in PRP17 map to the N-terminal nonconserved region of the protein, not to the WD (beta-transducin) repeat domain. The N-terminal domain mediates synthetic lethality with PRP16 and PRP18 mutations and shows allele-specific interactions with U5 snRNA (snr7 mutations), indicating this domain interacts functionally with other second-step factors and U5 snRNA. In vitro mutagenesis, genetic interaction analysis, synthetic lethality screens Genetics Medium 8722761
2000 PRP8 and PRP17/CDC40 have extensive genetic interactions: specific PRP8 mutations suppress the temperature-sensitive growth and splicing defects of prp17 null mutants, and suppress 3' splice site mutations. Conversely, other PRP8 alleles are synthetically lethal with prp17 absence. This supports a model where Prp8 and Prp17 interact functionally during the second catalytic step, particularly at the 3' splice site recognition stage. Genetic suppressor analysis, synthetic lethality screens, ACT1-CUP1 splicing reporter assay Genetics High 10628969
2001 SKY1 (a SRPK-family kinase) 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 splicing reporters, suggesting that Sky1p-mediated phosphorylation regulates the 3' AG recognition step in which Prp17 participates. Synthetic lethality analysis, ACT1-CUP1 splicing reporter assay RNA (New York, N.Y.) Medium 11565750
2003 PRP17/CDC40 is required for G1/S and G2/M cell cycle transitions. In prp17-null cells, splicing of TUB1 and TUB3 (alpha-tubulin) pre-mRNAs is specifically deficient; reduced alpha-tubulin protein underlies benomyl sensitivity and G2/M arrest. Genomic replacement with an intronless TUB1 gene relieves benomyl sensitivity, demonstrating that CDC40 controls mitosis through splicing of intron-containing tubulin genes. Cell cycle arrest/release experiments, in vitro splicing assays, intronless gene replacement, RT-PCR Nucleic acids research High 12711678
2004 CDC40/PRP17 controls cell cycle progression through splicing of the ANC1 pre-mRNA. Deletion of the ANC1 intron relieves G2/M arrest and temperature sensitivity of cdc40 mutants. Point mutation analysis of the ANC1 intron identified specific residues required for Cdc40p-dependent splicing, revealing a mechanism where cell cycle regulation depends on differential splicing of a subset of introns by specific splicing factors. Intron deletion rescue genetics, point mutation analysis of intron sequences, temperature-sensitivity assays Nucleic acids research High 15133121
2004 Genome-wide splicing microarray analysis shows that Prp17 is preferentially required for splicing of introns longer than 200 nt and is dispensable for introns with ≤13-nt spacing between branch point and 3' splice site. In vitro splicing with substrates of varying branch-to-3'SS distances confirmed these differential dependencies. In S. pombe, whose genome contains predominantly short introns, SpPrp17 is non-essential, linking the functional importance of this factor to intron architecture. Splicing-sensitive DNA microarrays, in vitro splicing assays with defined substrates, comparative genetics The Journal of biological chemistry High 15452114
2006 CDC40 (PRP17) is required for the G1/S transition (START) in addition to G2/M. Overexpression screening identified suppressors (chaperones, translation initiation factors, glycolytic enzymes) that relieve the G1/S transition delay of cdc40 cells. Enhanced temperature sensitivity of cdc40 combined with cln2Δ (G1 cyclin deletion) further supports a role for Cdc40p at START. cDNA overexpression suppressor screen, genetic interaction with cln2Δ, cell cycle timing assays Current genetics Medium 17171376
2008 Prp17 interacts with U2, U5, and U6 snRNPs (but is not a core component of any single snRNP) as shown by co-immunoprecipitation of snRNAs. Prp17 joins the spliceosome at the pre-catalytic A1 complex (after U4 dissociation) and remains through catalytic and post-splicing complexes containing the lariat intron. In prp17Δ extracts, stalled spliceosomes are compromised for the Prp16 helicase-triggered conformational switch required for step II. Co-immunoprecipitation with epitope-tagged Prp17, snRNA analysis, in vitro spliceosome assembly on actin pre-mRNA The Biochemical journal High 18691155
2020 Biallelic loss-of-function mutations in PRP17 (CDC40) cause autosomal-recessive pontocerebellar hypoplasia with microcephaly (PCHM) in humans. PPIL1 and PRP17 form an active isomerase-substrate interaction, but isomerase activity of PPIL1 is not critical for function. Loss of PRP17 affects splicing integrity, predominantly affecting short, high-GC-content introns and genes involved in brain disorders. Human genetics (biallelic mutations in patients), mouse knockouts (embryonic lethal), knockin patient mutation mice (neuron-specific apoptosis), splicing analysis Neuron High 33220177
2016 In hepatocellular carcinoma cells, CDC40 is upregulated by HBx-induced miR-1269b (miR-1269b paradoxically increases CDC40 protein despite being a miRNA). CDC40 overexpression increases cell cycle progression, cell proliferation, and migration in HCC cells. Western blot, colony formation, flow cytometry, cell migration assays, rescue experiments Journal of translational medicine Medium 27349221
2025 CDC40 knockdown in lung cancer cell lines induces cell cycle defects, growth inhibition, and apoptosis. Mechanistically, CDC40 loss causes retention of the first intron of CDCA5 pre-mRNA, leading to increased unspliced CDCA5 transcript and decreased CDCA5 protein expression. Protein-protein interaction analysis identifies spliceosome components as the main CDC40 binding partners in human cells. siRNA knockdown, global transcriptomics and splicing analysis, RT-PCR validation of CDCA5 intron retention, co-immunoprecipitation/proteomics for interaction partners Scientific reports Medium 39747150
2024 Among 18 spliceosome components analyzed, CDC40 depletion (along with AQR, SF3B1, SF3B4) may have a more direct role in nonsense-mediated mRNA decay (NMD) beyond indirect effects of general splicing perturbation, as suggested by transcriptome-wide analysis of NMD-targeted mRNA isoform upregulation. Bioinformatic analysis of publicly available RNA-seq datasets from cells depleted of spliceosome components bioRxivpreprint Low

Source papers

Stage 0 corpus · 47 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2006 Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2861 17081983
2012 Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 1718 22658674
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2015 The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 1118 26186194
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2003 Complete sequencing and characterization of 21,243 full-length human cDNAs. Nature genetics 754 14702039
2002 Comprehensive proteomic analysis of the human spliceosome. Nature 725 12226669
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2008 Genome-scale RNAi screen for host factors required for HIV replication. Cell host & microbe 627 18976975
2018 High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies. Molecular cell 580 29395067
2005 High-throughput mapping of a dynamic signaling network in mammalian cells. Science (New York, N.Y.) 553 15761153
2017 Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15. Science (New York, N.Y.) 533 28302793
1994 Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 492 8125298
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2010 Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science (New York, N.Y.) 421 20360068
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
1996 Normalization and subtraction: two approaches to facilitate gene discovery. Genome research 401 8889548
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
2012 Dynamic protein-protein interaction wiring of the human spliceosome. Molecular cell 318 22365833
2002 Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. RNA (New York, N.Y.) 301 11991638
1997 Binding specificity and in vivo targets of the EH domain, a novel protein-protein interaction module. Genes & development 290 9303539
2012 The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus. Cell 272 23084401
2016 The cell proliferation antigen Ki-67 organises heterochromatin. eLife 265 26949251
2017 A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis. Molecular cell 248 28431233
1999 The structural basis for the recognition of diverse receptor sequences by TRAF2. Molecular cell 248 10518213
2003 The DNA sequence and analysis of human chromosome 6. Nature 242 14574404
2018 Mapping the Genetic Landscape of Human Cells. Cell 225 30033366
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 46 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 33 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 0 39747150