{"gene":"PPIH","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2000,"finding":"Crystal structure of SnuCyp-20 (PPIH) determined at 2.0-Å resolution; the catalytic center superimposes with human cyclophilin A (hCypA), consistent with its observed peptidyl-prolyl cis/trans isomerase (PPIase) activity. An enlarged loop (alpha1-beta3), created by a five-amino-acid insertion unique to SnuCyp-20, forms a wide hydrophobic cleft proposed to mediate interaction with the U4/U6-60kD protein (PRPF4 ortholog).","method":"X-ray crystallography (2.0 Å, molecular replacement); PPIase activity assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic-resolution crystal structure combined with enzymatic activity assay; replicated and extended by subsequent mutagenesis study (PMID:12907720)","pmids":["10713041"],"is_preprint":false},{"year":2003,"finding":"Recombinant hCypH (PPIH) exhibits PPIase activity sharing the canonical catalytic pocket with other cyclophilins, but neither PPIase activity nor the catalytic pocket is required for stable binding to U4/U6 60K (PRPF4). Instead, a small insertion in a surface loop creates a second, distinct protein–protein interaction site that mediates specific, stable association with 60K, making PPIH the first small cyclophilin shown to have two protein–protein interaction surfaces.","method":"Recombinant protein expression and PPIase activity assay; site-directed mutagenesis of catalytic pocket and loop insertion; binding assays with 60K protein","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro activity assay plus mutagenesis of two distinct sites, multiple orthogonal approaches in one study, consistent with crystal structure data","pmids":["12907720"],"is_preprint":false},{"year":2017,"finding":"PPIH interacts with the N-terminus of PRPF4 (60K ortholog) through two distinct binding sites (bipartite interaction); the PRPF4 N-terminal region is intrinsically disordered and does not adopt secondary structure upon PPIH binding. Mutations at both sites are necessary to fully disrupt the complex, indicating that both sites contribute independently to complex stability.","method":"Recombinant protein expression and purification; complex formation assay; mutational analysis (point mutations uncoupling each binding site); biophysical characterization of PRPF4 N-terminus disorder","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal mutational analysis with purified proteins in a single lab; no structural data to atomic resolution, but multiple binding and mutagenesis experiments","pmids":["28935721"],"is_preprint":false}],"current_model":"PPIH (SnuCyp-20/CypH) is a nuclear cyclophilin component of the U4/U6 snRNP that possesses PPIase activity through a canonical catalytic pocket structurally homologous to cyclophilin A, but stably associates with U4/U6 core protein PRPF4 (60K) via a second, distinct protein–protein interaction surface created by a loop insertion, with the bipartite PPIH–PRPF4 interaction mediated by the intrinsically disordered N-terminus of PRPF4."},"narrative":{"mechanistic_narrative":"PPIH (SnuCyp-20/CypH) is a nuclear cyclophilin that functions as a stable component of the U4/U6 snRNP, where it bridges its intrinsic enzymatic identity with a dedicated structural role in spliceosomal protein assembly [PMID:10713041, PMID:12907720]. Its catalytic center superimposes on human cyclophilin A and confers peptidyl-prolyl cis/trans isomerase activity, but this catalytic pocket is dispensable for its defining interaction [PMID:10713041, PMID:12907720]. Instead, a five-amino-acid insertion unique to PPIH creates an enlarged surface loop forming a hydrophobic cleft that constitutes a second, distinct protein-protein interaction surface, making PPIH the first small cyclophilin shown to carry two independent protein-binding faces [PMID:10713041, PMID:12907720]. Through this arrangement PPIH binds the U4/U6 core protein PRPF4 (60K) in a bipartite manner, engaging the intrinsically disordered N-terminus of PRPF4 at two independent sites that each contribute to complex stability, with disruption requiring mutation of both [PMID:28935721]. Beyond the structural and biochemical characterization of the PPIH-PRPF4 interaction, no further mechanistic detail has been characterized in the available corpus.","teleology":[{"year":2000,"claim":"Established the structural basis of PPIH by showing its catalytic center matches cyclophilin A while revealing a unique insertion-generated surface feature, raising the question of whether this feature mediates spliceosomal partner binding.","evidence":"X-ray crystallography at 2.0 Å with molecular replacement and a PPIase activity assay","pmids":["10713041"],"confidence":"High","gaps":["Did not directly demonstrate that the loop cleft mediates 60K/PRPF4 binding","No mutagenesis to separate catalytic from binding functions"]},{"year":2003,"claim":"Resolved whether catalytic activity drives partner association by showing that neither the PPIase activity nor the catalytic pocket is needed for stable 60K binding, which instead uses a distinct second interaction surface.","evidence":"Recombinant PPIase assays plus site-directed mutagenesis of the catalytic pocket and loop insertion with 60K binding assays","pmids":["12907720"],"confidence":"High","gaps":["Did not define the molecular geometry of the second interaction site","Role of PPIase activity within the assembled snRNP not addressed"]},{"year":2017,"claim":"Defined the architecture of the PPIH-PRPF4 interaction as bipartite, engaging an intrinsically disordered PRPF4 N-terminus at two independently contributing sites required together for full complex stability.","evidence":"Recombinant protein complex formation and reciprocal point-mutation uncoupling of each binding site, with biophysical characterization of PRPF4 N-terminal disorder","pmids":["28935721"],"confidence":"Medium","gaps":["No atomic-resolution structure of the bipartite complex","Single-lab characterization without orthogonal in-cell validation","Functional consequence of bipartite binding for spliceosome assembly untested"]},{"year":null,"claim":"The catalytic (PPIase) function of PPIH within the assembled spliceosome and its substrates remain unidentified.","evidence":"","pmids":[],"confidence":"Low","gaps":["No physiological PPIase substrate identified","Role of isomerase activity in U4/U6 snRNP function unknown","No cellular phenotype or disease link characterized in the corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016853","term_label":"isomerase activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,2]}],"localization":[],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1]}],"complexes":["U4/U6 snRNP"],"partners":["PRPF4"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O43447","full_name":"Peptidyl-prolyl cis-trans isomerase H","aliases":["Rotamase H","Small nuclear ribonucleoprotein particle-specific cyclophilin H","CypH","U-snRNP-associated cyclophilin SnuCyp-20","USA-CYP"],"length_aa":177,"mass_kda":19.2,"function":"PPIase that catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides and may therefore assist protein folding (PubMed:20676357). Participates in pre-mRNA splicing. May play a role in the assembly of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome. May act as a chaperone","subcellular_location":"Nucleus speckle; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/O43447/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PPIH","classification":"Not Classified","n_dependent_lines":583,"n_total_lines":1208,"dependency_fraction":0.4826158940397351},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"PRPF4B","stoichiometry":4.0},{"gene":"CPSF6","stoichiometry":0.2},{"gene":"DDX21","stoichiometry":0.2},{"gene":"EFTUD2","stoichiometry":0.2},{"gene":"PRPF8","stoichiometry":0.2},{"gene":"RBM39","stoichiometry":0.2},{"gene":"RBM42","stoichiometry":0.2},{"gene":"SF3A1","stoichiometry":0.2},{"gene":"SNRPB","stoichiometry":0.2},{"gene":"SNRPC","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/PPIH","total_profiled":1310},"omim":[{"mim_id":"606095","title":"PEPTIDYL-PROLYL ISOMERASE H; PPIH","url":"https://www.omim.org/entry/606095"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PPIH"},"hgnc":{"alias_symbol":["USA-CYP","CYP-20","SnuCyp-20","CYPH","MGC5016"],"prev_symbol":[]},"alphafold":{"accession":"O43447","domains":[{"cath_id":"2.40.100.10","chopping":"12-175","consensus_level":"high","plddt":97.386,"start":12,"end":175}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O43447","model_url":"https://alphafold.ebi.ac.uk/files/AF-O43447-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O43447-F1-predicted_aligned_error_v6.png","plddt_mean":96.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PPIH","jax_strain_url":"https://www.jax.org/strain/search?query=PPIH"},"sequence":{"accession":"O43447","fasta_url":"https://rest.uniprot.org/uniprotkb/O43447.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O43447/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O43447"}},"corpus_meta":[{"pmid":"10713041","id":"PMC_10713041","title":"Crystal structure of the human U4/U6 small nuclear ribonucleoprotein particle-specific SnuCyp-20, a nuclear cyclophilin.","date":"2000","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/10713041","citation_count":26,"is_preprint":false},{"pmid":"35659370","id":"PMC_35659370","title":"The CYP/20-HETE/GPR75 axis in hypertension.","date":"2022","source":"Advances in pharmacology (San Diego, Calif.)","url":"https://pubmed.ncbi.nlm.nih.gov/35659370","citation_count":24,"is_preprint":false},{"pmid":"12907720","id":"PMC_12907720","title":"Two protein-protein interaction sites on the spliceosome-associated human cyclophilin CypH.","date":"2003","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/12907720","citation_count":20,"is_preprint":false},{"pmid":"38834966","id":"PMC_38834966","title":"PPIH acts as a potential predictive biomarker for patients with common solid tumors.","date":"2024","source":"BMC cancer","url":"https://pubmed.ncbi.nlm.nih.gov/38834966","citation_count":10,"is_preprint":false},{"pmid":"28935721","id":"PMC_28935721","title":"The spliceosomal proteins PPIH and PRPF4 exhibit bi-partite binding.","date":"2017","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/28935721","citation_count":9,"is_preprint":false},{"pmid":"39679070","id":"PMC_39679070","title":"PPIH Expression Correlates with Tumor Aggressiveness and Immune Dysregulation in Hepatocellular Carcinoma.","date":"2024","source":"Journal of hepatocellular carcinoma","url":"https://pubmed.ncbi.nlm.nih.gov/39679070","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5080,"output_tokens":967,"usd":0.014873,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7476,"output_tokens":1535,"usd":0.037878,"stage2_stop_reason":"end_turn"},"total_usd":0.052751,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2000,\n      \"finding\": \"Crystal structure of SnuCyp-20 (PPIH) determined at 2.0-Å resolution; the catalytic center superimposes with human cyclophilin A (hCypA), consistent with its observed peptidyl-prolyl cis/trans isomerase (PPIase) activity. An enlarged loop (alpha1-beta3), created by a five-amino-acid insertion unique to SnuCyp-20, forms a wide hydrophobic cleft proposed to mediate interaction with the U4/U6-60kD protein (PRPF4 ortholog).\",\n      \"method\": \"X-ray crystallography (2.0 Å, molecular replacement); PPIase activity assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic-resolution crystal structure combined with enzymatic activity assay; replicated and extended by subsequent mutagenesis study (PMID:12907720)\",\n      \"pmids\": [\"10713041\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Recombinant hCypH (PPIH) exhibits PPIase activity sharing the canonical catalytic pocket with other cyclophilins, but neither PPIase activity nor the catalytic pocket is required for stable binding to U4/U6 60K (PRPF4). Instead, a small insertion in a surface loop creates a second, distinct protein–protein interaction site that mediates specific, stable association with 60K, making PPIH the first small cyclophilin shown to have two protein–protein interaction surfaces.\",\n      \"method\": \"Recombinant protein expression and PPIase activity assay; site-directed mutagenesis of catalytic pocket and loop insertion; binding assays with 60K protein\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro activity assay plus mutagenesis of two distinct sites, multiple orthogonal approaches in one study, consistent with crystal structure data\",\n      \"pmids\": [\"12907720\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"PPIH interacts with the N-terminus of PRPF4 (60K ortholog) through two distinct binding sites (bipartite interaction); the PRPF4 N-terminal region is intrinsically disordered and does not adopt secondary structure upon PPIH binding. Mutations at both sites are necessary to fully disrupt the complex, indicating that both sites contribute independently to complex stability.\",\n      \"method\": \"Recombinant protein expression and purification; complex formation assay; mutational analysis (point mutations uncoupling each binding site); biophysical characterization of PRPF4 N-terminus disorder\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal mutational analysis with purified proteins in a single lab; no structural data to atomic resolution, but multiple binding and mutagenesis experiments\",\n      \"pmids\": [\"28935721\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PPIH (SnuCyp-20/CypH) is a nuclear cyclophilin component of the U4/U6 snRNP that possesses PPIase activity through a canonical catalytic pocket structurally homologous to cyclophilin A, but stably associates with U4/U6 core protein PRPF4 (60K) via a second, distinct protein–protein interaction surface created by a loop insertion, with the bipartite PPIH–PRPF4 interaction mediated by the intrinsically disordered N-terminus of PRPF4.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PPIH (SnuCyp-20/CypH) is a nuclear cyclophilin that functions as a stable component of the U4/U6 snRNP, where it bridges its intrinsic enzymatic identity with a dedicated structural role in spliceosomal protein assembly [#0, #1]. Its catalytic center superimposes on human cyclophilin A and confers peptidyl-prolyl cis/trans isomerase activity, but this catalytic pocket is dispensable for its defining interaction [#0, #1]. Instead, a five-amino-acid insertion unique to PPIH creates an enlarged surface loop forming a hydrophobic cleft that constitutes a second, distinct protein-protein interaction surface, making PPIH the first small cyclophilin shown to carry two independent protein-binding faces [#0, #1]. Through this arrangement PPIH binds the U4/U6 core protein PRPF4 (60K) in a bipartite manner, engaging the intrinsically disordered N-terminus of PRPF4 at two independent sites that each contribute to complex stability, with disruption requiring mutation of both [#2]. Beyond the structural and biochemical characterization of the PPIH-PRPF4 interaction, no further mechanistic detail has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Established the structural basis of PPIH by showing its catalytic center matches cyclophilin A while revealing a unique insertion-generated surface feature, raising the question of whether this feature mediates spliceosomal partner binding.\",\n      \"evidence\": \"X-ray crystallography at 2.0 Å with molecular replacement and a PPIase activity assay\",\n      \"pmids\": [\"10713041\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not directly demonstrate that the loop cleft mediates 60K/PRPF4 binding\", \"No mutagenesis to separate catalytic from binding functions\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Resolved whether catalytic activity drives partner association by showing that neither the PPIase activity nor the catalytic pocket is needed for stable 60K binding, which instead uses a distinct second interaction surface.\",\n      \"evidence\": \"Recombinant PPIase assays plus site-directed mutagenesis of the catalytic pocket and loop insertion with 60K binding assays\",\n      \"pmids\": [\"12907720\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the molecular geometry of the second interaction site\", \"Role of PPIase activity within the assembled snRNP not addressed\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined the architecture of the PPIH-PRPF4 interaction as bipartite, engaging an intrinsically disordered PRPF4 N-terminus at two independently contributing sites required together for full complex stability.\",\n      \"evidence\": \"Recombinant protein complex formation and reciprocal point-mutation uncoupling of each binding site, with biophysical characterization of PRPF4 N-terminal disorder\",\n      \"pmids\": [\"28935721\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No atomic-resolution structure of the bipartite complex\", \"Single-lab characterization without orthogonal in-cell validation\", \"Functional consequence of bipartite binding for spliceosome assembly untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The catalytic (PPIase) function of PPIH within the assembled spliceosome and its substrates remain unidentified.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No physiological PPIase substrate identified\", \"Role of isomerase activity in U4/U6 snRNP function unknown\", \"No cellular phenotype or disease link characterized in the corpus\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016853\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [\"U4/U6 snRNP\"],\n    \"partners\": [\"PRPF4\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}