CWC27 (also known as NY-CO-10 and SDCCAG10) is a nuclear, spliceosome-associated protein of the cyclophilin-type peptidyl-prolyl isomerase (PPIase) family. It has an N-terminal cyclophilin-like domain followed by a long disordered, partly coiled-coil C-terminal region. Although it belongs to the cyclophilin family, the CWC27 cyclophilin domain is a degenerate (catalytically inactive) pseudo-enzyme: it carries a glutamate in place of a conserved active-site residue and shows no detectable peptidyl-prolyl cis-trans isomerase activity and no cyclosporin binding. Functionally, CWC27 is a structural/scaffold component of the spliceosome. It is recruited during spliceosome activation as part of the activated Bact complex of the major (U2-type) spliceosome and is among the first factors released during the Bact-to-B* transition; it is also a component of the activated minor (U12-type) spliceosome, contributing to splicing of U12-type introns. In the major spliceosome the endonuclease-like domain of PRP8 contacts CWC27, and CWC27 works with its partner CWC22 in pre-mRNA splicing and exon junction complex deposition. Biallelic loss-of-function variants in CWC27 cause autosomal-recessive retinitis pigmentosa with or without skeletal and other developmental anomalies (RPSKA), underscoring its essential role in pre-mRNA splicing.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0071013 catalytic step 2 spliceosome | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic (IBA) inference that CWC27 is part of the catalytic step 2 spliceosome, transferred across the Cwc27 ortholog tree. CWC27 is genuinely a spliceosome component, but cryo-EM evidence places it specifically in the activated Bact (U2-type precatalytic-to-activated) stage, from which it is released before the step 2 (C*) reaction. Reason: CWC27 is correctly a spliceosomal component, so the broad family-level placement in a catalytic spliceosome is not wrong. However, structural studies show CWC27/NY-CO-10 is recruited to the activated Bact complex and released during the Bact-to-B* transition, so it is not specifically a step 2 catalytic spliceosome factor. Retained as a non-core membership term; the more precise activated-spliceosome terms (GO:0071005, GO:0005681) better capture its role. Supporting Evidence: PMID:29360106 the late Bact complex no longer contains the splicing factors RNF113A (Cwc24 in yeast) and NY-CO-10 (Cwc27 in yeast) |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Automated (IEA) annotation of nuclear localization, consistent with CWC27's role as a spliceosomal protein and with UniProt's curated subcellular location (Nucleus). Reason: Nuclear localization is well supported. UniProt records the subcellular location as Nucleus, and CWC27 is a component of nuclear spliceosomal complexes. More specific nucleoplasm annotations (GO:0005654) are also present. Supporting Evidence: file:human/CWC27/CWC27-uniprot.txt SUBCELLULAR LOCATION: Nucleus {ECO:0000305|PubMed:29360106}. |
| GO:0006457 protein folding | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro2GO (IEA) transfer of protein folding based solely on the cyclophilin-type PPIase InterPro signature (IPR020892). This is a family-level inference that assumes foldase/chaperone activity from domain membership. Reason: CWC27 is a demonstrated catalytically inactive pseudo-PPIase: it shows no peptidyl-prolyl cis-trans isomerase activity and no cyclosporin binding, and UniProt curates it as a "Probable inactive peptidyl-prolyl cis-trans isomerase" with a CAUTION. The InterPro2GO "protein folding" transfer ignores the loss of catalytic residues and therefore over-annotates a foldase/chaperone function that CWC27 does not possess. There is no evidence CWC27 catalyzes or assists protein folding. Supporting Evidence: PMID:20676357 No binding was detected for PPIL2, PPIL6, or SDCCAG-10, making these, to our knowledge, the first set of human cyclophilins that have been found incompetent to ligate cyclosporin file:human/CWC27/CWC27-uniprot.txt Despite the fact that it belongs to the cyclophilin-type PPIase family, a report has shown that it has probably no peptidyl-prolyl cis-trans isomerase activity. file:human/CWC27/CWC27-deep-research-falcon.md This loss of catalytic function is directly attributable to the Glu122 substitution in the active site, which renders the enzyme incompetent for proline isomerization |
| GO:0000398 mRNA splicing, via spliceosome | NAS PMID:29360106 Structure of the human activated spliceosome in three confor... | ACCEPT | Summary: NAS annotation (ComplexPortal) that CWC27 functions in pre-mRNA splicing via the spliceosome, based on its presence in the activated major spliceosome. Reason: mRNA splicing via the spliceosome is the core biological process of CWC27. CWC27/NY-CO-10 is a component of the activated (Bact) major spliceosome resolved by cryo-EM, and biallelic loss of function causes a Mendelian disease consistent with impaired splicing. As a non-catalytic scaffold, CWC27 also forms a heterodimer with CWC22 that the falcon deep research describes as a landing platform coupling spliceosome activation to eIF4A3/exon junction complex recruitment, consistent with its splicing role. Supporting Evidence: PMID:29360106 the late Bact complex no longer contains the splicing factors RNF113A (Cwc24 in yeast) and NY-CO-10 (Cwc27 in yeast) file:human/CWC27/CWC27-deep-research-falcon.md A critical function of CWC27 is its formation of a heterodimer with CWC22, another spliceosomal protein |
| GO:0000398 mRNA splicing, via spliceosome | NAS PMID:33509932 Structure of the activated human minor spliceosome. | ACCEPT | Summary: NAS annotation (ComplexPortal) that CWC27 functions in pre-mRNA splicing, based on its presence in the activated human minor (U12-type) spliceosome. Reason: CWC27 is a component of the activated minor spliceosome that splices U12-type introns, directly supporting its involvement in mRNA splicing via the spliceosome. Supporting Evidence: PMID:33509932 The minor spliceosome mediates splicing of the rare but essential U12-type precursor messenger RNA. |
| GO:0005681 spliceosomal complex | IPI PMID:39068178 Molecular basis for the activation of human spliceosome. | ACCEPT | Summary: IPI annotation (ComplexPortal) placing CWC27 as part of the spliceosomal complex, based on identification within activation-stage spliceosome structures. Reason: Spliceosome membership is directly and unambiguously supported by cryo-EM structures of the human spliceosome capturing the activation pathway (pre-Bact through post-Bact). This is a core cellular-component annotation for CWC27. Supporting Evidence: PMID:39068178 intermediate states between the B and B* complexes: pre-Bact, Bact-I, Bact-II, Bact-III, Bact-IV, and post-Bact |
| GO:0071018 U12-type catalytic step 2 spliceosome | IPI PMID:33509932 Structure of the activated human minor spliceosome. | KEEP AS NON CORE | Summary: IPI annotation placing CWC27 as part of the U12-type (minor) catalytic step 2 spliceosome, based on the cryo-EM structure of the activated human minor spliceosome. Reason: CWC27 is a genuine component of the activated minor spliceosome, so minor (U12-type) spliceosome membership is correct. Retained as non-core: as in the major spliceosome, CWC27 associates with the activated complex and the precise catalytic-step-2 placement is a curated mapping of the resolved minor spliceosome state rather than evidence of a step 2 catalytic role for CWC27. Supporting Evidence: PMID:33509932 Here, we report the atomic features of the activated human minor spliceosome determined by cryo-electron microscopy at 2.9-angstrom resolution. |
| GO:0005654 nucleoplasm | IDA GO_REF:0000052 | ACCEPT | Summary: IDA annotation (HPA immunofluorescence) localizing CWC27 to the nucleoplasm. Reason: Nucleoplasmic localization is consistent with CWC27's role as a spliceosomal protein and with the curated UniProt nuclear localization. Direct immunofluorescence evidence supports this subcellular component. Supporting Evidence: file:human/CWC27/CWC27-uniprot.txt SUBCELLULAR LOCATION: Nucleus {ECO:0000305|PubMed:29360106}. |
| GO:0000398 mRNA splicing, via spliceosome | IC PMID:29360106 Structure of the human activated spliceosome in three confor... | ACCEPT | Summary: IC annotation inferring involvement in mRNA splicing from membership in the U2-type precatalytic/activated spliceosome (GO:0071005). Reason: A sound curator inference: CWC27 is a structural component of the activated major spliceosome, so it is reasonably inferred to be involved in mRNA splicing via the spliceosome, the core process for this protein. Supporting Evidence: PMID:29360106 the late Bact complex no longer contains the splicing factors RNF113A (Cwc24 in yeast) and NY-CO-10 (Cwc27 in yeast) |
| GO:0071005 U2-type precatalytic spliceosome | IDA PMID:29360106 Structure of the human activated spliceosome in three confor... | ACCEPT | Summary: IDA annotation placing CWC27 in the U2-type (major) precatalytic/activated spliceosome, based on the cryo-EM structure of the human activated spliceosome. Reason: This is the most precisely evidenced cellular-component annotation for CWC27. Cryo-EM directly visualizes NY-CO-10 (CWC27) in the activated major (Bact) spliceosome, with the PRP8 endonuclease-like domain contacting it, and shows it is released during the Bact-to-B* transition. The falcon deep research adds the mechanistic detail that release is driven by the DEAH-box helicase PRP2 (with SPP2), which during the Bact-to-B* transition triggers dissociation of CWC27 along with the SF3a/SF3b and RES complexes. Supporting Evidence: PMID:29360106 the late Bact complex no longer contains the splicing factors RNF113A (Cwc24 in yeast) and NY-CO-10 (Cwc27 in yeast) file:human/CWC27/CWC27-deep-research-falcon.md The DEAH-box helicase PRP2, assisted by its co-activator SPP2, pulls on the 3' end of the intron, leading to dissociation of the SF3a/SF3b complexes, RES complex, and importantly, both CWC24 and CWC27 |
| GO:0003755 peptidyl-prolyl cis-trans isomerase activity | IDA NOT PMID:20676357 Structural and biochemical characterization of the human cyc... | ACCEPT | Summary: Negated (NOT) IDA annotation recording that CWC27 (SDCCAG-10) does NOT have peptidyl-prolyl cis-trans isomerase activity, based on direct biochemical assay showing no tetrapeptide isomerase activity and no cyclosporin binding. Reason: This negated annotation correctly captures the experimental finding that CWC27 is a catalytically inactive pseudo-PPIase. Davis et al. found SDCCAG-10 (CWC27) incompetent for both cyclosporin binding and tetrapeptide isomerase activity, attributable to a glutamate substitution at a conserved active-site position. The NOT annotation should be retained as it documents the absence of the family-expected catalytic activity. Supporting Evidence: PMID:20676357 No binding was detected for PPIL2, PPIL6, or SDCCAG-10, making these, to our knowledge, the first set of human cyclophilins that have been found incompetent to ligate cyclosporin |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-9770131 | ACCEPT | Summary: TAS annotation (Reactome, Formation of the Spliceosomal B* complex) localizing CWC27 to the nucleoplasm. Reason: Nucleoplasmic localization is consistent with CWC27's spliceosomal function and with the curated UniProt nuclear localization and HPA immunofluorescence evidence. Supporting Evidence: file:human/CWC27/CWC27-uniprot.txt SUBCELLULAR LOCATION: Nucleus {ECO:0000305|PubMed:29360106}. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-9770145 | ACCEPT | Summary: TAS annotation (Reactome, Formation of the Spliceosomal Bact complex) localizing CWC27 to the nucleoplasm. Reason: Consistent with CWC27's recruitment into the activated Bact spliceosome in the nucleoplasm; supported by curated nuclear localization and immunofluorescence. Supporting Evidence: file:human/CWC27/CWC27-uniprot.txt SUBCELLULAR LOCATION: Nucleus {ECO:0000305|PubMed:29360106}. |
| GO:0005654 nucleoplasm | TAS Reactome:R-HSA-9921507 | ACCEPT | Summary: TAS annotation (Reactome, NS5 interacts with Spliceosome) localizing CWC27 to the nucleoplasm. Reason: Nucleoplasmic localization is well supported for this spliceosomal protein. The annotation derives from a Reactome pathway in which the spliceosome (with CWC27) resides in the nucleoplasm. Supporting Evidence: file:human/CWC27/CWC27-uniprot.txt SUBCELLULAR LOCATION: Nucleus {ECO:0000305|PubMed:29360106}. |
| GO:0000398 mRNA splicing, via spliceosome | IC PMID:11991638 Purification and characterization of native spliceosomes sui... | ACCEPT | Summary: IC annotation inferring involvement in mRNA splicing from CWC27's presence in native purified spliceosomes (catalytic step 2 / C-complex-enriched). Reason: CWC27 is detected in native purified spliceosomes, supporting the inference that it participates in mRNA splicing via the spliceosome, its core process. Supporting Evidence: PMID:11991638 These spliceosomes consist largely of C complex containing splicing |
| GO:0071013 catalytic step 2 spliceosome | IDA PMID:11991638 Purification and characterization of native spliceosomes sui... | KEEP AS NON CORE | Summary: IDA annotation placing CWC27 in the catalytic step 2 spliceosome, based on its identification in native purified C-complex-enriched spliceosomes. Reason: CWC27 was detected in native purified spliceosome preparations enriched for C complex, supporting spliceosome membership. However, higher-resolution cryo-EM work later localized CWC27/NY-CO-10 specifically to the activated Bact stage, from which it is released before step 2 catalysis. The catalytic step 2 placement reflects the bulk composition of the purified preparation rather than a specific step 2 role, so it is retained as a non-core membership term. Supporting Evidence: PMID:11991638 These spliceosomes consist largely of C complex containing splicing PMID:29360106 the late Bact complex no longer contains the splicing factors RNF113A (Cwc24 in yeast) and NY-CO-10 (Cwc27 in yeast) |
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Download this section (compressed HTML)Q: Does the catalytically dead cyclophilin domain of CWC27 retain a substrate-binding or proline-recognition function within the spliceosome that contributes to splice site fidelity, even in the absence of isomerase catalysis?
Q: How does the CWC27-CWC22 module mechanistically couple spliceosome activation to positioning of eIF4A3/the exon junction complex, and which step of EJC deposition requires CWC27?
Q: Why do CWC27 loss-of-function variants produce a retina-predominant phenotype (RPSKA) despite ubiquitous expression and an essential splicing role?
Experiment: Structure-guided mutagenesis of the degenerate active-site residue(s) (e.g., the Glu at the position equivalent to PPIA Trp121) combined with rescue assays in CWC27-null cells to test whether restoring a canonical cyclophilin active site confers PPIase activity and/or alters splicing.
Experiment: Transcriptome-wide splicing analysis (RNA-seq/junction analysis) in CWC27-depleted cells, with emphasis on U12-type minor introns and retina-expressed transcripts, to define the set of introns dependent on CWC27.
Experiment: Cross-linking/proteomics and cryo-EM of the CWC27-CWC22 sub-complex bound to eIF4A3 to map the interface and test the model that CWC27 positions the EJC core for deposition during splicing.
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