Affinage

PRPF40A

Pre-mRNA-processing factor 40 homolog A · UniProt O75400

Round 2 corrected
Length
957 aa
Mass
108.8 kDa
Annotated
2026-04-28
74 papers in source corpus 8 papers cited in narrative 9 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

PRPF40A is a nuclear splicing factor that promotes early spliceosome assembly by bridging 5′ and 3′ splice-site recognition components through its tandem WW domains, which engage proline-rich motifs in SF1 and SF3A1 at the E and A complex stages; selectivity for these partners is enforced by an intramolecular autoinhibitory interaction between the WW tandem and PRPF40A's own N-terminal proline-rich region (PMID:38719828). Functionally, PRPF40A acts predominantly as an activator of cassette exon inclusion—especially for exons flanked by short, GC-rich introns—and is globally required for microexon splicing, co-regulating this program with SRRM4 (PMID:38943321, PMID:39389624). PRPF40A localizes to nuclear speckles and its cytoplasmic sequestration by polyglutamine-expanded huntingtin impairs pre-mRNA splicing, linking PRPF40A mislocalization to Huntington's disease-associated RNA processing defects (PMID:21566141, PMID:9700202). Loss of PRPF40A in hematopoietic cells causes increased cell death and reduced proliferation, with cell death partially rescued by its paralog PRPF40B (PMID:38943321).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 1998 Medium

    Identification of PRPF40A as a WW-domain protein that binds huntingtin's proline-rich region established its first molecular interaction and implicated it in spliceosome-related biology, though its precise splicing function was unknown.

    Evidence Yeast two-hybrid screen and binding confirmed in HD lymphoblastoid cell extracts

    PMID:9700202

    Open questions at the time
    • No direct evidence of splicing function at this stage
    • Interaction with huntingtin not validated by reciprocal IP from endogenous sources
    • Polyglutamine-length dependence mechanism unclear
  2. 2004 Medium

    Demonstration that PRPF40A sequesters N-WASP in the nucleus and suppresses EGF-induced actin microspike formation revealed a non-canonical function in controlling cytoplasmic actin dynamics via subcellular partitioning of a binding partner.

    Evidence Transient transfection, confocal immunofluorescence, and EGF stimulation assay in COS7 cells

    PMID:14697212

    Open questions at the time
    • Endogenous N-WASP nuclear retention by PRPF40A not shown under physiological conditions
    • Relevance to splicing function unclear
    • Single cell type tested
  3. 2005 Medium

    Co-purification of PRPF40A with the nuclear scaffold protein NAKAP and their co-localization in Huntington's disease nuclear aggregates suggested PRPF40A forms part of a nuclear docking platform that is disrupted by mutant huntingtin.

    Evidence Yeast two-hybrid, in vitro binding, nuclear matrix fractionation, and immunofluorescence in HD patient neurons

    PMID:16391387

    Open questions at the time
    • Functional consequence of NAKAP-PRPF40A interaction on splicing not tested
    • Co-localization in aggregates does not prove functional sequestration
    • Single lab, no independent replication
  4. 2006 High

    Determination of the NMR structure of PRPF40A's first WW domain and mapping of its proline-rich peptide binding grooves established the molecular basis for its Group-II/III WW domain specificity.

    Evidence Solution NMR structure and 1H-15N HSQC chemical shift perturbation titration

    PMID:16463264

    Open questions at the time
    • Only WW1 solved; tandem WW domain architecture unknown at this point
    • Binding to physiological spliceosomal partners not yet demonstrated structurally
    • No cellular functional validation of identified binding grooves
  5. 2011 High

    Structural and functional evidence that polyglutamine-expanded huntingtin sequesters PRPF40A to the cytoplasm via cooperative binding of the huntingtin proline-rich region to the WW tandem, directly reducing pre-mRNA splicing efficiency, provided the first mechanistic link between PRPF40A mislocalization and Huntington's disease-associated splicing defects.

    Evidence NMR of WW-PRR interaction, cellular fractionation, splicing efficiency assays, immunofluorescence

    PMID:21566141

    Open questions at the time
    • Splicing defects not mapped to specific target transcripts
    • In vivo relevance in HD model organisms not tested
    • Whether PRPF40B can compensate for PRPF40A mislocalization unknown
  6. 2024 High

    Transcriptome-wide characterization revealed PRPF40A as an activator of cassette exon inclusion for exons with short, GC-rich flanking introns and as a factor essential for cell viability in hematopoietic cells, with partial functional overlap with PRPF40B.

    Evidence siRNA knockdown in HL-60 cells, RNA-seq, rescue with PRPF40B overexpression, nuclear speckle localization analysis

    PMID:38943321

    Open questions at the time
    • Mechanism by which GC-richness or intron length determines PRPF40A dependence not elucidated
    • Tissue-specificity of PRPF40A requirement beyond HL-60 cells unclear
    • Extent of functional redundancy with PRPF40B for splicing targets unknown
  7. 2024 High

    Structural determination of the PRPF40A tandem WW domains and discovery of an intramolecular autoinhibitory mechanism by its own proline-rich region explained how PRPF40A selectively engages high-affinity spliceosomal partners SF1 and SF3A1 to bridge 5′ and 3′ splice-site recognition during early spliceosome assembly.

    Evidence NMR, SAXS, ITC, mutational analysis, and immunoprecipitation in cells

    PMID:38719828

    Open questions at the time
    • Structural basis of autoinhibition release upon partner engagement not fully resolved
    • No cryo-EM or crystal structure of PRPF40A within the spliceosome
    • Whether autoinhibition is regulated by post-translational modification unknown
  8. 2024 High

    PRPF40A was shown to be globally required for microexon splicing with a graded size dependence, and to engage in homeostatic cross-regulation with spliceosomal partner Luc7l, revealing an unexpected feedback circuit between functionally coupled spliceosomal factors.

    Evidence siRNA knockdown in mouse neuroblastoma cells, RNA-seq, comparison with SRRM4 knockdown datasets

    PMID:39389624

    Open questions at the time
    • Molecular mechanism by which PRPF40A preferentially supports microexon recognition unknown
    • Whether PRPF40A-Luc7l cross-regulation occurs in human neurons not tested
    • Contribution of PRPF40A to neurodevelopmental microexon programs in vivo uncharacterized

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key unresolved questions include the structural basis of PRPF40A within assembled spliceosomal complexes, the molecular determinants of its microexon selectivity, whether post-translational modifications regulate autoinhibition, and the in vivo contribution of PRPF40A mislocalization to Huntington's disease pathology.
  • No cryo-EM structure of PRPF40A in spliceosomal context
  • In vivo HD model studies with PRPF40A manipulation absent
  • Post-translational regulation of autoinhibitory mechanism untested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 3 GO:0060090 molecular adaptor activity 1
Localization
GO:0005634 nucleus 4 GO:0005654 nucleoplasm 2
Pathway
R-HSA-8953854 Metabolism of RNA 4
Partners
HTTLUC7LNAKAPSF1SF3A1SRRM4WASL

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1998 PRPF40A (HYPA/FBP11) was identified as a WW domain-containing protein that binds huntingtin's proline-rich N-terminal region via its WW domains. The interaction is enhanced by lengthening the adjacent polyglutamine tract and is mediated by huntingtin's proline-rich region. HYPA was recognized as a protein implicated in spliceosome function, establishing its role as an RNA processing factor. Yeast two-hybrid screen, confirmed by interaction with huntingtin in extracts of HD lymphoblastoid cells Human molecular genetics Medium 9700202
2004 FBP11 (PRPF40A) sequesters N-WASP in the nucleus, thereby inhibiting N-WASP-dependent actin microspike formation in the cytoplasm. Endogenous FBP11 localizes to nuclear speckles, and co-expression with N-WASP leads to nuclear co-localization. EGF-induced microspike formation was suppressed by FBP11 overexpression, demonstrating that FBP11 negatively regulates cytoplasmic N-WASP function by controlling its subcellular localization. Transient transfection, confocal immunofluorescence, EGF stimulation assay in COS7 cells, loss-of-function/gain-of-function with defined phenotypic readout Biochemical and biophysical research communications Medium 14697212
2005 PRPF40A (HypA/FBP11) interacts with the nuclear scaffold protein NAKAP via a proline-rich domain in NAKAP engaging a WW domain of PRPF40A. Both NAKAP and PRPF40A co-purify with the nuclear matrix in cultured cells and in human brain, and NAKAP associates with PRPF40A from HD patient brain tissue where they co-localize with mutant huntingtin in nuclear aggregates, suggesting PRPF40A-NAKAP forms a nuclear docking scaffold for huntingtin. Yeast two-hybrid, in vitro binding assay, deletion mapping, co-purification with nuclear matrix fraction, immunofluorescence in HD neurons Neuromolecular medicine Medium 16391387
2006 The first WW domain of FBP11/HYPA (PRPF40A) adopts an antiparallel triple-stranded beta-sheet with XP and XP2 grooves on its surface. NMR titration showed the WW domain binds proline-rich peptides containing PL, PP, and PR motifs, with the XP2 groove being functionally important for ligand recognition, establishing PRPF40A as a Group-II/III WW domain protein with broad proline-rich motif binding specificity. Solution NMR structure determination, 1H-15N HSQC chemical shift perturbation titration Proteins High 16463264
2011 Polyglutamine-expanded huntingtin sequesters PRPF40A (HYPA/FBP11) to cytosolic locations and significantly reduces pre-mRNA splicing efficiency. NMR structural analysis showed that the proline-rich region (PRR) of huntingtin cooperatively interacts with PRPF40A's tandem WW domains through a domain-chaperoning effect of WW1 on WW2, establishing a mechanism whereby polyQ-expanded Htt causes dysfunction of cellular RNA processing by mislocating PRPF40A. NMR structural analysis of WW domain-PRR interaction, cellular fractionation, pre-mRNA splicing efficiency assays, immunofluorescence co-localization The Journal of biological chemistry High 21566141
2024 PRPF40A acts predominantly as an activator of cassette exon inclusion, particularly for exons flanked by short, GC-rich introns that tend to localize to nuclear speckles in the nuclear center. PRPF40A knockdown in HL-60 cells caused increased cell death, decreased proliferation, and a slight differentiation phenotype with upregulation of immune activation genes. Cell death but not proliferation defects were rescued by overexpression of its paralog PRPF40B. PRPF40A shares regulatory features with SRRM2, SON, PCBP1/2, TRA2B, and SRSF2, forming a functional network regulating splicing partly via co-localization in the nucleus. siRNA knockdown in HL-60 cells, transcriptomic (RNA-seq) analysis, rescue experiments with PRPF40B overexpression, nuclear speckle localization analysis Nucleic acids research High 38943321
2024 The PRPF40A tandem WW domains adopt a specific solution structure (determined by NMR and SAXS) in which both WW domains cooperate to bind high-affinity SF1 proline-rich peptide, enabling tryptophan sandwiching by two proline residues. Unexpectedly, a proline-rich motif in the N-terminal region of PRPF40A itself mediates intramolecular interactions with the WW tandem, acting as an autoinhibitory filter that selectively gates binding to high-affinity proline-rich motifs in bona fide partners such as SF1 and SF3A1. This autoinhibitory mechanism was validated by NMR, ITC, mutational analysis in vitro, and immunoprecipitation in cells, establishing that PRPF40A promotes spliceosome assembly at early E and A complexes by bridging 5' and 3' splice site recognition. NMR, SAXS, ITC, mutational analysis, immunoprecipitation in cells Nature communications High 38719828
2024 PRPF40A is globally required for microexon splicing in mouse neuroblastoma cells, with dependence on PRPF40A exhibiting a graded decrease as exon size increases (rather than a sharp threshold). PRPF40A co-regulates microexons together with SRRM4, a neuron-specific microexon regulator. Additionally, PRPF40A knockdown causes increased productive splicing of its spliceosomal binding partner Luc7l by skipping a small poison exon, revealing homeostatic cross-regulation between functionally coupled but evolutionarily unrelated spliceosomal components. siRNA knockdown in mouse neuroblastoma cells, RNA-seq, comparison with SRRM4 knockdown datasets RNA (New York, N.Y.) High 39389624
2025 In yeast, Prp40 (the PRPF40A ortholog) is stably associated with U1 snRNP and multiple domains of Prp40 directly interact with RNA polymerase II independently of the pol II CTD. In contrast, human PRPF40A and PRPF40B are alternative splicing factors that are not integral components of U1 snRNP, indicating a functional divergence of Prp40 homologs during evolution: the transcription-splicing coupling function shifted from Prp40/PRPF40A to U1-70K in humans. Co-immunoprecipitation of yeast snRNPs with pol II, domain-deletion analysis of Prp40, comparison with human PRPF40A behavior bioRxivpreprint Medium

Source papers

Stage 0 corpus · 74 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
2005 A human protein-protein interaction network: a resource for annotating the proteome. Cell 1704 16169070
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
2004 Large-scale characterization of HeLa cell nuclear phosphoproteins. Proceedings of the National Academy of Sciences of the United States of America 1159 15302935
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
2014 A proteome-scale map of the human interactome network. Cell 977 25416956
2012 The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Molecular cell 973 22681889
2020 A reference map of the human binary protein interactome. Nature 849 32296183
2018 VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. Cell discovery 829 29507755
2003 Complete sequencing and characterization of 21,243 full-length human cDNAs. Nature genetics 754 14702039
2007 Large-scale mapping of human protein-protein interactions by mass spectrometry. Molecular systems biology 733 17353931
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2012 A census of human soluble protein complexes. Cell 689 22939629
2015 Gene essentiality and synthetic lethality in haploid human cells. Science (New York, N.Y.) 657 26472760
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2006 A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell 610 16713569
2018 High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies. Molecular cell 580 29395067
2017 Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15. Science (New York, N.Y.) 533 28302793
2021 Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV. Nature 532 33845483
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2011 The Brd4 extraterminal domain confers transcription activation independent of pTEFb by recruiting multiple proteins, including NSD3. Molecular and cellular biology 437 21555454
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
2004 Proteomic, functional, and domain-based analysis of in vivo 14-3-3 binding proteins involved in cytoskeletal regulation and cellular organization. Current biology : CB 386 15324660
2003 Degradation of Cdc25A by beta-TrCP during S phase and in response to DNA damage. Nature 380 14603323
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
2004 A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease. Molecular cell 339 15383276
1998 Huntingtin interacts with a family of WW domain proteins. Human molecular genetics 338 9700202
1995 The petunia MADS box gene FBP11 determines ovule identity. The Plant cell 270 8535139
2001 Requirement of nickel metabolism proteins HypA and HypB for full activity of both hydrogenase and urease in Helicobacter pylori. Molecular microbiology 155 11123699
2002 Network of hydrogenase maturation in Escherichia coli: role of accessory proteins HypA and HybF. Journal of bacteriology 79 12081959
1996 The Agaricus bisporus hypA gene encodes a hydrophobin and specifically accumulates in peel tissue of mushroom caps during fruit body development. Journal of molecular biology 73 8632464
2009 Structure of a nickel chaperone, HypA, from Helicobacter pylori reveals two distinct metal binding sites. Journal of the American Chemical Society 64 19621959
2017 COL1A1, PRPF40A, and UCP2 correlate with hypoxia markers in non-small cell lung cancer. Journal of cancer research and clinical oncology 57 28258342
2005 Escherichia coli HypA is a zinc metalloprotein with a weak affinity for nickel. Journal of bacteriology 54 15995183
2011 Metallo-GTPase HypB from Helicobacter pylori and its interaction with nickel chaperone protein HypA. The Journal of biological chemistry 46 22179820
2010 Communication between the zinc and nickel sites in dimeric HypA: metal recognition and pH sensing. Journal of the American Chemical Society 45 20662514
2006 Mutagenesis of hydrogenase accessory genes of Synechocystis sp. PCC 6803. Additional homologues of hypA and hypB are not active in hydrogenase maturation. The FEBS journal 42 16972939
2016 Mechanism of Selective Nickel Transfer from HypB to HypA, Escherichia coli [NiFe]-Hydrogenase Accessory Proteins. Biochemistry 38 27951644
2007 Interaction between the Helicobacter pylori accessory proteins HypA and UreE is needed for urease maturation. Microbiology (Reading, England) 38 17464061
2004 Aspergillus nidulans hypA regulates morphogenesis through the secretion pathway. Fungal genetics and biology : FG & B 35 14643261
2013 Metal transfer within the Escherichia coli HypB-HypA complex of hydrogenase accessory proteins. Biochemistry 34 23899293
2011 Protein interactions and localization of the Escherichia coli accessory protein HypA during nickel insertion to [NiFe] hydrogenase. The Journal of biological chemistry 34 22016389
2014 Nickel translocation between metallochaperones HypA and UreE in Helicobacter pylori. Metallomics : integrated biometal science 29 25010720
2012 The Arthroderma benhamiae hydrophobin HypA mediates hydrophobicity and influences recognition by human immune effector cells. Eukaryotic cell 29 22408226
2011 Interaction with polyglutamine-expanded huntingtin alters cellular distribution and RNA processing of huntingtin yeast two-hybrid protein A (HYPA). The Journal of biological chemistry 26 21566141
2012 Helicobacter pylori hydrogenase accessory protein HypA and urease accessory protein UreG compete with each other for UreE recognition. Biochimica et biophysica acta 25 22698670
2007 A dynamic Zn site in Helicobacter pylori HypA: a potential mechanism for metal-specific protein activity. Journal of the American Chemical Society 25 17199266
1994 Nucleotide sequences of two hydrogenase-related genes (hypA and hypB) from Bradyrhizobium japonicum, one of which (hypB) encodes an extremely histidine-rich region and guanine nucleotide-binding domains. Biochimica et biophysica acta 21 8305450
2006 Solution structure and binding specificity of FBP11/HYPA WW domain as Group-II/III. Proteins 19 16463264
2004 FBP11 regulates nuclear localization of N-WASP and inhibits N-WASP-dependent microspike formation. Biochemical and biophysical research communications 19 14697212
2015 Dynamic HypA zinc site is essential for acid viability and proper urease maturation in Helicobacter pylori. Metallomics : integrated biometal science 18 25608738
2017 Structure-function analyses of metal-binding sites of HypA reveal residues important for hydrogenase maturation in Helicobacter pylori. PloS one 16 28809946
2017 Nickel Ligation of the N-Terminal Amine of HypA Is Required for Urease Maturation in Helicobacter pylori. Biochemistry 15 28177601
2018 Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools. Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry 14 30264175
2018 The Helicobacter pylori HypA·UreE2 Complex Contains a Novel High-Affinity Ni(II)-Binding Site. Biochemistry 13 29708738
2005 Association of HYPA haplotype in the mannose-binding lectin gene-2 with Behçet's disease. Tissue antigens 12 15730518
2005 Interaction of the nuclear matrix protein NAKAP with HypA and huntingtin: implications for nuclear toxicity in Huntington's disease pathogenesis. Neuromolecular medicine 11 16391387
2019 Bimodal Nickel-Binding Site on Escherichia coli [NiFe]-Hydrogenase Metallochaperone HypA. Inorganic chemistry 10 31273981
2013 The zinc-binding fragment of HypA from Helicobacter pylori: a tempting site also for nickel ions. Dalton transactions (Cambridge, England : 2003) 10 23338727
2019 The Metallochaperone Encoding Gene hypA Is Widely Distributed among Pathogenic Aeromonas spp. and Its Expression Is Increased under Acidic pH and within Macrophages. Microorganisms 9 31581740
2015 Specificity of the Zn(2+), Cd(2+) and Ni(2+) ion binding sites in the loop domain of the HypA protein. Dalton transactions (Cambridge, England : 2003) 7 25945782
2024 PRPF40A induces inclusion of exons in GC-rich regions important for human myeloid cell differentiation. Nucleic acids research 6 38943321
2023 The structure of the high-affinity nickel-binding site in the Ni,Zn-HypA•UreE2 complex. Metallomics : integrated biometal science 6 36638839
2006 Expression and purification of active WW domains of FBP11/HYPA and FBP28/CA150. Protein and peptide letters 6 16472085
1998 Rhizobium leguminosarum bv. viciae hypA gene is specifically expressed in pea (Pisum sativum) bacteroids and required for hydrogenase activity and processing. FEMS microbiology letters 5 9868773
2024 Intramolecular autoinhibition regulates the selectivity of PRPF40A tandem WW domains for proline-rich motifs. Nature communications 4 38719828
2013 Mannose-binding lectin genetic analysis: possible protective role of the HYPA haplotype in the development of recurrent urinary tract infections in men. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 3 24321858
2024 Conserved role for spliceosomal component PRPF40A in microexon splicing. RNA (New York, N.Y.) 2 39389624
2026 Dose-dependent biphasic effect of environmental UVA on stem cell function through PRPF40A, TGF-β1, NFATc1 signaling. Journal of photochemistry and photobiology. B, Biology 0 41950867
2026 The HypA and HypB metallochaperones from Methanococcus maripaludis have unique metal-binding properties and a distinct nickel transfer mechanism. The Journal of biological chemistry 0 42001940
2024 Conserved role for spliceosomal component PRPF40A in microexon splicing. bioRxiv : the preprint server for biology 0 39386728