{"gene":"FKBP3","run_date":"2026-04-28T17:46:03","timeline":{"discoveries":[{"year":1992,"finding":"FKBP25 (FKBP3) was cloned and shown to have peptidylprolyl cis-trans isomerase (PPIase) activity, with higher affinity for rapamycin (IC50 = 50 nM) than FK506 (IC50 = 400 nM). The C-terminal 97 amino acids share identity with FKBP12 and FKBP13, and the sequence contains putative nuclear localization signals.","method":"Molecular cloning, recombinant protein expression, in vitro PPIase activity assay with inhibitor titration","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — in vitro enzymatic assay with quantitative inhibition data, foundational cloning paper","pmids":["1375932"],"is_preprint":false},{"year":1993,"finding":"FKBP25 is predominantly nuclear in T-lymphoma Jurkat cells and has the ability to bind DNA; the FKBP25/DNA complex is dissociated by high salt. The N-terminal domain is predicted to form an amphipathic helix-loop-helix that may account for DNA binding, while FKBP12 (lacking this N-terminal region) does not bind DNA.","method":"Cell fractionation, Western blotting, DNA-binding assay, CD spectroscopy","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 — direct fractionation and DNA-binding experiment, but single lab with limited mutagenesis follow-up","pmids":["8422914"],"is_preprint":false},{"year":1999,"finding":"FKBP25 (FKBP3) expression is transcriptionally repressed following p53 induction in both human and murine cell lines after DNA damage.","method":"Differential gene expression screening, Northern/Western blot after p53 induction by DNA damage stimuli","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 3 — expression-level evidence in multiple cell lines after p53 induction, but mechanism of repression not dissected","pmids":["10557083"],"is_preprint":false},{"year":2009,"finding":"FKBP25 interacts with MDM2, stimulates MDM2 auto-ubiquitylation and proteasomal degradation, leading to p53 activation. siRNA-mediated depletion of FKBP25 increases MDM2 levels and reduces p53 and p21 levels.","method":"Co-immunoprecipitation, siRNA knockdown, ubiquitylation assay, Western blotting","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal Co-IP and functional siRNA knockdown with defined molecular readouts, single lab","pmids":["19166840"],"is_preprint":false},{"year":2014,"finding":"FKBP25 interacts with nucleolin in an rRNA-dependent manner and associates with the immature pre-60S ribosomal subunit in nuclear extract but not with mature ribosomes, implicating FKBP25 in ribosome biogenesis. The proteomic analysis also identified interactions with ribosomal proteins, ribosomal processing factors, and chromatin modifiers.","method":"Proteomic characterization (mass spectrometry), co-immunoprecipitation, sucrose gradient fractionation","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 — proteomic interactome plus reciprocal Co-IP with rRNA-dependency test and ribosomal fractionation","pmids":["24840943"],"is_preprint":false},{"year":2014,"finding":"The N-terminal domain of FKBP25 (residues 1-73) adopts a novel Basic Tilted Helix Bundle (BTHB) fold with a positively charged surface patch. This domain is proposed to mediate DNA binding, and YY1 can bind to this region, potentially regulating DNA binding.","method":"NMR/X-ray crystallography structural determination, sequence conservation analysis, binding assay with YY1","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 1 — structural determination of domain, but functional validation of BTHB-DNA binding is inferred rather than directly demonstrated by mutagenesis","pmids":["24667607"],"is_preprint":false},{"year":2014,"finding":"Endogenous FKBP25 associates with core histones of the nucleosome, spliceosomal complex components, and ribosomal subunits. FKBP25 is detected on polyribosomes, and its association is released by added RNA or 0.5 M NaCl, indicating RNA-dependent binding. Rapamycin/FK506 treatment causes residual release, suggesting some interactions also involve the PPIase cavity.","method":"Anti-FKBP25 immunoprecipitation, proteomics, polyribosome fractionation, RNA/salt dissociation experiments","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — multiple interaction partners identified by proteomics with functional dissociation experiments","pmids":["24998444"],"is_preprint":false},{"year":2016,"finding":"The NMR solution structure of full-length human FKBP25 reveals that the N-terminal helix-loop-helix (HLH) domain and C-terminal FKBD interact with each other. Both domains contribute to DNA binding: the HLH domain makes major-groove contacts, while the basic FKBD loop cooperates with adjacent minor-groove interactions. Mutational studies validated this model.","method":"NMR solution structure determination, mutational studies, DNA-binding assays","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 — full-length NMR structure with mutagenesis validation of DNA binding mechanism","pmids":["26762975"],"is_preprint":false},{"year":2016,"finding":"Crystal structure of the ternary complex FRB-rapamycin-FKBP25 was determined at 1.67-Å resolution, revealing rapamycin-induced physical interaction between FKBP25 and the FRB domain of mTOR. Conformational changes in FRB create a methionine-rich hole and covalent metalloid coordination at C2085 of FRB was observed.","method":"Proximity biotin-labeling (pBirA), immunoprecipitation, immunofluorescence, X-ray crystallography (1.67 Å)","journal":"ACS central science","confidence":"High","confidence_rationale":"Tier 1 — crystal structure of ternary complex plus orthogonal proximity labeling and Co-IP validation","pmids":["27610411"],"is_preprint":false},{"year":2013,"finding":"Mutagenesis of the FKBP25 catalytic domain distinguishes domain-destabilizing mutations from 'surgical' mutations that ablate PPIase activity while maintaining domain fold, providing tools to differentiate catalytic versus non-catalytic functions.","method":"Site-directed mutagenesis, in vitro PPIase activity assay, domain folding assessment","journal":"Biochemical Society transactions","confidence":"Medium","confidence_rationale":"Tier 1 — in vitro mutagenesis and functional characterization, single lab review/methods paper","pmids":["23697935"],"is_preprint":false},{"year":2017,"finding":"FKBP25 promotes cell proliferation in non-small cell lung cancer through a Sp1/HDAC2/p27 axis: FKBP3 inhibits ubiquitination of the transcription factor Sp1, stabilizing it to drive HDAC2 promoter activity; HDAC2 then modulates histone H3K4 acetylation at the p27 promoter to suppress p27 expression.","method":"siRNA knockdown, overexpression, ChIP, luciferase reporter assay, ubiquitination assay, xenograft in vivo model","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal methods (ChIP, reporter, ubiquitination assay) in a single lab","pmids":["28839465"],"is_preprint":false},{"year":2017,"finding":"The N-terminal BTHB domain of FKBP25 specifically binds double-stranded RNA (dsRNA) over single-stranded RNA or DNA. This RNA-binding activity is required for FKBP25 nucleolar localization and for the vast majority of its protein interactions including those with 60S pre-ribosome and early ribosome biogenesis factors. The BTHB and FKBP domains have independent mobility, suggesting the N-terminus anchors to dsRNA while the catalytic domain interacts with neighboring proteins.","method":"NMR spectroscopy, RNA binding assays (EMSA and fluorescence), mutagenesis, nucleolar localization imaging, proteomic interaction mapping","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 — NMR structural data, mutagenesis, and multiple orthogonal assays confirming dsRNA-binding and functional localization consequence","pmids":["29036638"],"is_preprint":false},{"year":2018,"finding":"FKBP25 directly binds microtubules via its catalytic FKBP domain to promote microtubule polymerization and stabilize the MT network. FKBP25 associates with the mitotic spindle and regulates entry into mitosis. Depletion leads to increased chromosome instability. Additionally, Protein Kinase C phosphorylates FKBP25 to disrupt its chromatin association during mitosis while maintaining spindle interaction.","method":"In vitro microtubule binding and polymerization assay, live cell imaging, knockdown with chromosome instability readout, PKC phosphorylation assay, domain mapping","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1–2 — direct in vitro MT binding/polymerization assay, live cell imaging of spindle association, PKC phosphorylation with defined functional consequence","pmids":["29361176"],"is_preprint":false},{"year":2019,"finding":"FKBP25 promotes homologous recombination (HR) and suppresses single-strand annealing (SSA) in DNA double-strand break repair. Depletion reduces Rad51 repair foci after etoposide and ionizing radiation. The PPIase catalytic activity of FKBP25 is required for this HR-promoting function. Rapamycin impairs HR at least partly independently of mTOR.","method":"siRNA knockdown, DSB repair reporter assays, Rad51 foci imaging, rapamycin treatment, catalytic mutant rescue experiments","journal":"Biochemistry and cell biology","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal DSB repair assays with catalytic mutant demonstrating requirement for enzymatic activity","pmids":["30620620"],"is_preprint":false},{"year":2015,"finding":"FKBP25 interacts with TRPC6 and regulates non-capacitative calcium entry (NCCE) in platelets and HEK-293 cells. FK506 modifies the association pattern between FKBP25 and TRPC channels. siRNA silencing of FKBP25 inhibits OAG-evoked NCCE, and FKBP25 is found at the plasma membrane by biotinylation experiments.","method":"Co-immunoprecipitation, siRNA knockdown, calcium flux assay, biotinylation/surface protein isolation, TRPC6-/- mouse platelets","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP interaction plus functional knockdown phenotype with knockout mouse validation, single lab","pmids":["26239116"],"is_preprint":false},{"year":2021,"finding":"FKBP3 promotes HIV-1 latency by binding to YY1 (indirect association with the HIV-1 LTR) and recruiting HDAC1/2 to the viral LTR, inducing histone deacetylation. FKBP3 knockout in latently infected cell lines promotes latent HIV-1 activation.","method":"CRISPR knockout in latent HIV-1 cell lines, co-immunoprecipitation (FKBP3-YY1), ChIP (HDAC1/2 at LTR), latent HIV-1 reactivation assays, primary latent cell model","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal Co-IP and ChIP with CRISPR KO functional validation, single lab","pmids":["34281390"],"is_preprint":false},{"year":2021,"finding":"ESD (esterase D) interacts with FKBP25 via the FKBP25 N-terminus (1-90 aa), reduces K48-linked polyubiquitination of FKBP25 thereby stabilizing cytoplasmic FKBP25, and promotes FKBP25 binding to mTORC1, suppressing mTORC1 activity and inducing autophagy.","method":"Yeast two-hybrid, co-immunoprecipitation, ubiquitination assay (K48 linkage-specific), mTORC1 substrate phosphorylation (P70S6K, 4EBP1), autophagy assay","journal":"Cellular & molecular biology letters","confidence":"Medium","confidence_rationale":"Tier 2 — yeast two-hybrid plus Co-IP with functional mTORC1 suppression readout, single lab","pmids":["34875997"],"is_preprint":false},{"year":2018,"finding":"FKBP25 translocates to the nucleus under ischemic (OGD) or peroxynitrite stress conditions in endothelial cells, where it interacts with 60S ribosomal protein L7a. FKBP25 overexpression protects endothelial cells against OGD injury.","method":"Western blot, immunofluorescence, co-immunoprecipitation, FRET, overexpression rescue assay","journal":"Cellular physiology and biochemistry","confidence":"Low","confidence_rationale":"Tier 3 — single Co-IP/FRET interaction with limited mechanistic follow-up, single lab","pmids":["29969783"],"is_preprint":false},{"year":2021,"finding":"FKBP25 depletion in mouse oocytes causes abnormal spindle assembly, chromosome misalignment, and defective kinetochore-microtubule attachment, leading to elevated aneuploidy. Serine 163 is identified as a major phosphorylation site modulating FKBP25 function in meiotic maturation.","method":"siRNA knockdown in mouse oocytes, immunofluorescence (spindle/chromosome), aneuploidy quantification, site-directed mutagenesis (S163A)","journal":"Frontiers in cell and developmental biology","confidence":"Medium","confidence_rationale":"Tier 2 — loss-of-function with defined spindle/chromosome phenotype plus phospho-site mutagenesis, single lab","pmids":["33553183"],"is_preprint":false},{"year":2023,"finding":"FKBP3 interacts with PARK7 (DJ-1); FKBP3 knockdown enhances PARK7 ubiquitination and degradation. FKBP3 activates the Wnt/β-catenin signaling pathway through PARK7. FOXO3 binds the FKBP3 promoter to suppress its transcription.","method":"Co-immunoprecipitation, ubiquitination assay, ChIP (FOXO3 at FKBP3 promoter), Wnt/β-catenin pathway reporters, xenograft model","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP plus ubiquitination assay and ChIP, single lab","pmids":["37987202"],"is_preprint":false},{"year":2023,"finding":"FKBP25 knockdown in C2C12 myoblasts increases cell viability/accumulation and migration independent of tubulin dynamics, demonstrating a role in myoblast behavior distinct from its previously described microtubule-regulatory function.","method":"Doxycycline-inducible shRNA knockdown, cell viability assay, migration assay, tubulin dynamics analysis","journal":"The FEBS journal","confidence":"Low","confidence_rationale":"Tier 3 — single lab, knockdown with cellular phenotype but no direct molecular mechanism identified","pmids":["37345229"],"is_preprint":false}],"current_model":"FKBP25 (encoded by FKBP3) is a nuclear prolyl isomerase with a C-terminal FK506-binding/PPIase domain and an N-terminal Basic Tilted Helix Bundle (BTHB) domain that selectively binds double-stranded RNA to direct nucleolar localization and ribosome biogenesis interactions; the catalytic domain binds microtubules to promote polymerization and spindle integrity, catalytic PPIase activity promotes homologous recombination in DSB repair, chromatin association is cell-cycle regulated by PKC phosphorylation, FKBP25 stabilizes MDM2 auto-ubiquitylation to activate p53, recruits HDAC1/2 via YY1 to repress target loci (including HIV-1 LTR), drives HDAC2 expression through Sp1 stabilization to control cell proliferation, and forms a rapamycin-induced ternary complex with the mTOR FRB domain to modulate mTORC1 signaling."},"narrative":{"teleology":[{"year":1992,"claim":"Identification of FKBP25 as a nuclear immunophilin with PPIase activity and preferential rapamycin binding established that the FKBP family extends to the nucleus with distinct pharmacological properties.","evidence":"Molecular cloning with recombinant PPIase assay and inhibitor IC50 determination","pmids":["1375932"],"confidence":"High","gaps":["No in vivo substrates for PPIase activity identified","Nuclear localization signals predicted but not functionally validated"]},{"year":1993,"claim":"Demonstration that FKBP25 is predominantly nuclear and binds DNA via its unique N-terminal domain distinguished it from cytoplasmic FKBPs and suggested a chromatin-regulatory function.","evidence":"Cell fractionation of Jurkat cells, DNA-binding assay, CD spectroscopy","pmids":["8422914"],"confidence":"Medium","gaps":["DNA-binding specificity (sequence or structure preference) not defined","No mutagenesis to confirm N-terminal domain necessity"]},{"year":2009,"claim":"Discovery that FKBP25 stimulates MDM2 auto-ubiquitylation and degradation, thereby activating p53, revealed FKBP25 as a regulator of the p53 tumor-suppressor pathway.","evidence":"Reciprocal co-immunoprecipitation, siRNA knockdown, ubiquitylation assay","pmids":["19166840"],"confidence":"Medium","gaps":["Whether PPIase catalytic activity is required for MDM2 interaction not tested","In vivo relevance to tumor suppression not established","Earlier observation that p53 represses FKBP25 transcription (PMID:10557083) suggests a feedback loop whose mechanism is undefined"]},{"year":2014,"claim":"Proteomic and structural studies collectively revealed that FKBP25 associates with pre-60S ribosomal subunits in an RNA-dependent manner and that its N-terminal domain adopts a novel BTHB fold, reframing the protein as a ribosome biogenesis factor with a structurally unique nucleic acid-binding module.","evidence":"Mass spectrometry interactome, sucrose gradient fractionation, NMR/X-ray crystallography of BTHB domain, RNA/salt dissociation experiments","pmids":["24840943","24667607","24998444"],"confidence":"High","gaps":["Direct substrates of PPIase activity during ribosome maturation unknown","Whether BTHB binds RNA or DNA in vivo was unresolved at this point"]},{"year":2016,"claim":"Full-length NMR structure showed both BTHB and FKBP domains cooperate for DNA binding via major- and minor-groove contacts, and the crystal structure of a rapamycin-bridged FRB–FKBP25 ternary complex established a structural basis for rapamycin-dependent mTOR engagement.","evidence":"NMR solution structure with mutagenesis validation of DNA contacts; 1.67-Å crystal structure of FRB–rapamycin–FKBP25 plus proximity labeling","pmids":["26762975","27610411"],"confidence":"High","gaps":["Physiological significance of FKBP25–mTOR interaction without exogenous rapamycin unclear","Genomic targets of FKBP25 DNA binding not mapped"]},{"year":2017,"claim":"The BTHB domain was shown to be a dsRNA-specific binder whose RNA-binding activity directs nucleolar localization and mediates nearly all protein interactions, resolving the question of whether the N-terminus primarily engages DNA or RNA in vivo.","evidence":"NMR, EMSA and fluorescence RNA-binding assays, mutagenesis, nucleolar imaging, proteomic interaction mapping","pmids":["29036638"],"confidence":"High","gaps":["Specific dsRNA targets in the nucleolus not identified","Relative contribution of DNA- versus RNA-binding to chromatin functions unresolved"]},{"year":2017,"claim":"FKBP25 was shown to promote NSCLC cell proliferation through a Sp1/HDAC2/p27 axis, where it stabilizes Sp1 to drive HDAC2 transcription and epigenetically silence the cell-cycle inhibitor p27.","evidence":"siRNA/overexpression, ChIP, luciferase reporter, ubiquitination assay, xenograft model","pmids":["28839465"],"confidence":"Medium","gaps":["Whether PPIase activity is required for Sp1 stabilization not tested","Generalizability beyond NSCLC cell lines unclear"]},{"year":2018,"claim":"The catalytic FKBP domain was found to directly bind microtubules and promote polymerization, while PKC phosphorylation releases FKBP25 from chromatin during mitosis, establishing a dual nuclear/cytoskeletal role regulated by cell-cycle-dependent phosphorylation.","evidence":"In vitro MT binding/polymerization, live cell spindle imaging, PKC phosphorylation assay, chromosome instability quantification upon depletion","pmids":["29361176"],"confidence":"High","gaps":["Identity of PKC isoform(s) responsible not determined","Structural basis for FKBP domain–tubulin interaction unknown"]},{"year":2019,"claim":"PPIase catalytic activity was directly demonstrated to be required for promoting homologous recombination and Rad51 focus formation at DSBs, establishing an enzymatic role in the DNA damage response.","evidence":"DSB repair reporter assays, Rad51 foci imaging, catalytic-dead mutant rescue experiments","pmids":["30620620"],"confidence":"High","gaps":["Direct proline-isomerization substrate in the HR pathway not identified","Rapamycin's HR-inhibitory effect was only partially mTOR-independent, leaving the mechanism unclear"]},{"year":2021,"claim":"FKBP25 was shown to recruit HDAC1/2 to the HIV-1 LTR via YY1 interaction, maintaining viral latency, while oocyte studies confirmed spindle and kinetochore-microtubule functions with identification of S163 as a regulatory phosphosite, and ESD was found to stabilize cytoplasmic FKBP25 to suppress mTORC1.","evidence":"CRISPR KO in latent HIV-1 cells with ChIP (PMID:34281390); siRNA in mouse oocytes with aneuploidy quantification and S163A mutagenesis (PMID:33553183); yeast two-hybrid/Co-IP with mTORC1 substrate phosphorylation readout (PMID:34875997)","pmids":["34281390","33553183","34875997"],"confidence":"Medium","gaps":["Whether FKBP25 isomerase activity is needed for YY1-HDAC recruitment unknown","How ESD-mediated stabilization relates to nuclear FKBP25 functions unaddressed","Direct FKBP25 phosphosite(s) for PKC versus the S163 site relationship not clarified"]},{"year":2023,"claim":"FKBP25 was linked to Wnt/β-catenin signaling through stabilization of PARK7/DJ-1, with FOXO3 acting as a transcriptional repressor of FKBP3, expanding its regulatory network.","evidence":"Co-IP, ubiquitination assay, ChIP of FOXO3 at FKBP3 promoter, Wnt reporter, xenograft model","pmids":["37987202"],"confidence":"Medium","gaps":["Whether PPIase activity mediates PARK7 stabilization untested","Relationship of PARK7-Wnt axis to FKBP25's nuclear and ribosomal functions unclear"]},{"year":null,"claim":"The direct in vivo substrates of FKBP25 PPIase activity across its diverse functions (HR repair, ribosome biogenesis, chromatin regulation, microtubule dynamics) remain unidentified, and the relative physiological importance of its DNA- versus dsRNA-binding modes is unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No proline-isomerization substrate identified in any pathway","Genome-wide binding profiles (ChIP-seq/CLIP-seq) not reported","No genetic mouse model phenotype characterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,9,13]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[11]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[1,7]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[12]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3,10,16]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,1,7,12]},{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[4,11]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[12,18]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[16]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[13]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[12,18]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[4,11]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[8,16]},{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[10,15]}],"complexes":["FRB-rapamycin-FKBP25 ternary complex","YY1-FKBP25-HDAC1/2 repressor complex","pre-60S ribosomal subunit"],"partners":["MDM2","YY1","HDAC1","HDAC2","NCL","TRPC6","ESD","PARK7"],"other_free_text":[]},"mechanistic_narrative":"FKBP25 (encoded by FKBP3) is a nuclear immunophilin that integrates peptidylprolyl cis-trans isomerase (PPIase) activity with nucleic acid binding to regulate ribosome biogenesis, chromatin dynamics, DNA repair, and mitotic spindle integrity. Its N-terminal Basic Tilted Helix Bundle (BTHB) domain selectively binds double-stranded RNA, which is required for nucleolar localization and association with pre-60S ribosomal subunits and ribosome biogenesis factors, while both the BTHB and C-terminal FKBP domains cooperate to bind DNA [PMID:29036638, PMID:26762975]. The catalytic FKBP domain directly binds microtubules to promote polymerization and spindle stability—with PKC phosphorylation releasing chromatin association during mitosis—and PPIase activity is required for promoting homologous recombination at DNA double-strand breaks [PMID:29361176, PMID:30620620]. FKBP25 also modulates signaling and transcription by stabilizing MDM2 auto-ubiquitylation to activate p53, recruiting HDAC1/2 via YY1 to repress target loci including the HIV-1 LTR, driving HDAC2 expression through Sp1 stabilization, and forming a rapamycin-induced ternary complex with the mTOR FRB domain [PMID:19166840, PMID:34281390, PMID:28839465, PMID:27610411]."},"prefetch_data":{"uniprot":{"accession":"Q00688","full_name":"Peptidyl-prolyl cis-trans isomerase FKBP3","aliases":["25 kDa FK506-binding protein","25 kDa FKBP","FKBP-25","FK506-binding protein 3","FKBP-3","Immunophilin FKBP25","Rapamycin-selective 25 kDa immunophilin","Rotamase"],"length_aa":224,"mass_kda":25.2,"function":"FK506- and rapamycin-binding proteins (FKBPs) constitute a family of receptors for the two immunosuppressants which inhibit T-cell proliferation by arresting two distinct cytoplasmic signal transmission pathways. PPIases accelerate the folding of proteins","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q00688/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/FKBP3","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/FKBP3","total_profiled":1310},"omim":[{"mim_id":"618649","title":"HECT DOMAIN E3 UBIQUITIN PROTEIN LIGASE 1; HECTD1","url":"https://www.omim.org/entry/618649"},{"mim_id":"186947","title":"FK506-BINDING PROTEIN 3; FKBP3","url":"https://www.omim.org/entry/186947"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"skeletal muscle","ntpm":397.6},{"tissue":"tongue","ntpm":347.3}],"url":"https://www.proteinatlas.org/search/FKBP3"},"hgnc":{"alias_symbol":["FKBP-25","FKBP25"],"prev_symbol":[]},"alphafold":{"accession":"Q00688","domains":[{"cath_id":"1.10.720.80","chopping":"11-68","consensus_level":"high","plddt":83.381,"start":11,"end":68},{"cath_id":"3.10.50.40","chopping":"110-222","consensus_level":"high","plddt":87.379,"start":110,"end":222}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q00688","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q00688-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q00688-F1-predicted_aligned_error_v6.png","plddt_mean":77.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=FKBP3","jax_strain_url":"https://www.jax.org/strain/search?query=FKBP3"},"sequence":{"accession":"Q00688","fasta_url":"https://rest.uniprot.org/uniprotkb/Q00688.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q00688/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q00688"}},"corpus_meta":[{"pmid":"10557083","id":"PMC_10557083","title":"Down-regulation of the stathmin/Op18 and FKBP25 genes following p53 induction.","date":"1999","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/10557083","citation_count":110,"is_preprint":false},{"pmid":"1375932","id":"PMC_1375932","title":"Molecular cloning of a 25-kDa high affinity rapamycin binding protein, FKBP25.","date":"1992","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/1375932","citation_count":77,"is_preprint":false},{"pmid":"19166840","id":"PMC_19166840","title":"FKBP25, a novel regulator of the p53 pathway, induces the degradation of MDM2 and activation of p53.","date":"2009","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/19166840","citation_count":58,"is_preprint":false},{"pmid":"28839465","id":"PMC_28839465","title":"FKBP3 Promotes Proliferation of Non-Small Cell Lung Cancer Cells through Regulating Sp1/HDAC2/p27.","date":"2017","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/28839465","citation_count":54,"is_preprint":false},{"pmid":"27610411","id":"PMC_27610411","title":"Proximity-Directed Labeling Reveals a New Rapamycin-Induced Heterodimer of FKBP25 and FRB in Live Cells.","date":"2016","source":"ACS central science","url":"https://pubmed.ncbi.nlm.nih.gov/27610411","citation_count":46,"is_preprint":false},{"pmid":"8422914","id":"PMC_8422914","title":"On the localization of FKBP25 in T-lymphocytes.","date":"1993","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/8422914","citation_count":43,"is_preprint":false},{"pmid":"31955008","id":"PMC_31955008","title":"Melatonin Regulates Breast Cancer Progression by the lnc010561/miR-30/FKBP3 Axis.","date":"2019","source":"Molecular therapy. Nucleic acids","url":"https://pubmed.ncbi.nlm.nih.gov/31955008","citation_count":32,"is_preprint":false},{"pmid":"31524278","id":"PMC_31524278","title":"FKBP3 mediates oxaliplatin resistance in colorectal cancer cells by regulating HDAC2 expression.","date":"2019","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/31524278","citation_count":27,"is_preprint":false},{"pmid":"26762975","id":"PMC_26762975","title":"Structural basis of nucleic acid recognition by FK506-binding protein 25 (FKBP25), a nuclear immunophilin.","date":"2016","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/26762975","citation_count":26,"is_preprint":false},{"pmid":"24840943","id":"PMC_24840943","title":"The prolyl isomerase, FKBP25, interacts with RNA-engaged nucleolin and the pre-60S ribosomal subunit.","date":"2014","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/24840943","citation_count":24,"is_preprint":false},{"pmid":"29361176","id":"PMC_29361176","title":"The prolyl isomerase FKBP25 regulates microtubule polymerization impacting cell cycle progression and genomic stability.","date":"2018","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/29361176","citation_count":17,"is_preprint":false},{"pmid":"24998444","id":"PMC_24998444","title":"Rapamycin-binding FKBP25 associates with diverse proteins that form large intracellular entities.","date":"2014","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/24998444","citation_count":14,"is_preprint":false},{"pmid":"10900128","id":"PMC_10900128","title":"Mammalian FKBP-25 and its associated proteins.","date":"2000","source":"Archives of biochemistry and biophysics","url":"https://pubmed.ncbi.nlm.nih.gov/10900128","citation_count":13,"is_preprint":false},{"pmid":"24667607","id":"PMC_24667607","title":"Basic Tilted Helix Bundle - a new protein fold in human FKBP25/FKBP3 and HectD1.","date":"2014","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/24667607","citation_count":13,"is_preprint":false},{"pmid":"29036638","id":"PMC_29036638","title":"The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module.","date":"2017","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/29036638","citation_count":13,"is_preprint":false},{"pmid":"23697935","id":"PMC_23697935","title":"Resolving the functions of peptidylprolyl isomerases: insights from the mutagenesis of the nuclear FKBP25 enzyme.","date":"2013","source":"Biochemical Society transactions","url":"https://pubmed.ncbi.nlm.nih.gov/23697935","citation_count":12,"is_preprint":false},{"pmid":"8876379","id":"PMC_8876379","title":"Cloning and high expression of rabbit FKBP25 in cornea.","date":"1996","source":"Japanese journal of ophthalmology","url":"https://pubmed.ncbi.nlm.nih.gov/8876379","citation_count":10,"is_preprint":false},{"pmid":"34875997","id":"PMC_34875997","title":"Esterase D stabilizes FKBP25 to suppress mTORC1.","date":"2021","source":"Cellular & molecular biology letters","url":"https://pubmed.ncbi.nlm.nih.gov/34875997","citation_count":9,"is_preprint":false},{"pmid":"26239116","id":"PMC_26239116","title":"FKBP25 and FKBP38 regulate non-capacitative calcium entry through TRPC6.","date":"2015","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/26239116","citation_count":9,"is_preprint":false},{"pmid":"30620620","id":"PMC_30620620","title":"FKBP25 participates in DNA double-strand break 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invasion and migration, deactivated NF-κB/IL-6 signaling pathway through inhibiting histone deacetylase 2 expression.","date":"2023","source":"The Chinese journal of physiology","url":"https://pubmed.ncbi.nlm.nih.gov/37082996","citation_count":6,"is_preprint":false},{"pmid":"15908283","id":"PMC_15908283","title":"Molecular cloning and expression pattern of the Fkbp25 gene during cerebral cortical neurogenesis.","date":"2005","source":"Gene expression patterns : GEP","url":"https://pubmed.ncbi.nlm.nih.gov/15908283","citation_count":6,"is_preprint":false},{"pmid":"12392168","id":"PMC_12392168","title":"Cloning and identification of a novel cDNA which may be associated with FKBP25.","date":"2002","source":"Biochemical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/12392168","citation_count":5,"is_preprint":false},{"pmid":"37987202","id":"PMC_37987202","title":"FKBP3 aggravates the malignant phenotype of diffuse large B-cell lymphoma by PARK7-mediated activation of Wnt/β-catenin signalling.","date":"2023","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/37987202","citation_count":4,"is_preprint":false},{"pmid":"33553183","id":"PMC_33553183","title":"FKBP25 Regulates Meiotic Apparatus During Mouse Oocyte Maturation.","date":"2021","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/33553183","citation_count":4,"is_preprint":false},{"pmid":"37345229","id":"PMC_37345229","title":"FKBP25 regulates myoblast viability and migration and is differentially expressed in in vivo models of muscle adaptation.","date":"2023","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/37345229","citation_count":1,"is_preprint":false},{"pmid":"37488794","id":"PMC_37488794","title":"[Procine recombinant NK-lysin inhibits hepatocellular carcinoma metastasis by downregulating FKBP3 and inhibiting oxidative phosphorylation and glycolysis: a proteomic analysis].","date":"2023","source":"Nan fang yi ke da xue xue bao = Journal of Southern Medical University","url":"https://pubmed.ncbi.nlm.nih.gov/37488794","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":14738,"output_tokens":5088,"usd":0.060267},"stage2":{"model":"claude-opus-4-6","input_tokens":8612,"output_tokens":3319,"usd":0.189053},"total_usd":0.24932,"stage1_batch_id":"msgbatch_0118RScg3WGaGkaZRtWZbtce","stage2_batch_id":"msgbatch_01Cpfzvtbj42aqp5oYZ5Te2s","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1992,\n      \"finding\": \"FKBP25 (FKBP3) was cloned and shown to have peptidylprolyl cis-trans isomerase (PPIase) activity, with higher affinity for rapamycin (IC50 = 50 nM) than FK506 (IC50 = 400 nM). The C-terminal 97 amino acids share identity with FKBP12 and FKBP13, and the sequence contains putative nuclear localization signals.\",\n      \"method\": \"Molecular cloning, recombinant protein expression, in vitro PPIase activity assay with inhibitor titration\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro enzymatic assay with quantitative inhibition data, foundational cloning paper\",\n      \"pmids\": [\"1375932\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"FKBP25 is predominantly nuclear in T-lymphoma Jurkat cells and has the ability to bind DNA; the FKBP25/DNA complex is dissociated by high salt. The N-terminal domain is predicted to form an amphipathic helix-loop-helix that may account for DNA binding, while FKBP12 (lacking this N-terminal region) does not bind DNA.\",\n      \"method\": \"Cell fractionation, Western blotting, DNA-binding assay, CD spectroscopy\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct fractionation and DNA-binding experiment, but single lab with limited mutagenesis follow-up\",\n      \"pmids\": [\"8422914\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"FKBP25 (FKBP3) expression is transcriptionally repressed following p53 induction in both human and murine cell lines after DNA damage.\",\n      \"method\": \"Differential gene expression screening, Northern/Western blot after p53 induction by DNA damage stimuli\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — expression-level evidence in multiple cell lines after p53 induction, but mechanism of repression not dissected\",\n      \"pmids\": [\"10557083\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"FKBP25 interacts with MDM2, stimulates MDM2 auto-ubiquitylation and proteasomal degradation, leading to p53 activation. siRNA-mediated depletion of FKBP25 increases MDM2 levels and reduces p53 and p21 levels.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, ubiquitylation assay, Western blotting\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP and functional siRNA knockdown with defined molecular readouts, single lab\",\n      \"pmids\": [\"19166840\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"FKBP25 interacts with nucleolin in an rRNA-dependent manner and associates with the immature pre-60S ribosomal subunit in nuclear extract but not with mature ribosomes, implicating FKBP25 in ribosome biogenesis. The proteomic analysis also identified interactions with ribosomal proteins, ribosomal processing factors, and chromatin modifiers.\",\n      \"method\": \"Proteomic characterization (mass spectrometry), co-immunoprecipitation, sucrose gradient fractionation\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — proteomic interactome plus reciprocal Co-IP with rRNA-dependency test and ribosomal fractionation\",\n      \"pmids\": [\"24840943\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"The N-terminal domain of FKBP25 (residues 1-73) adopts a novel Basic Tilted Helix Bundle (BTHB) fold with a positively charged surface patch. This domain is proposed to mediate DNA binding, and YY1 can bind to this region, potentially regulating DNA binding.\",\n      \"method\": \"NMR/X-ray crystallography structural determination, sequence conservation analysis, binding assay with YY1\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 — structural determination of domain, but functional validation of BTHB-DNA binding is inferred rather than directly demonstrated by mutagenesis\",\n      \"pmids\": [\"24667607\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Endogenous FKBP25 associates with core histones of the nucleosome, spliceosomal complex components, and ribosomal subunits. FKBP25 is detected on polyribosomes, and its association is released by added RNA or 0.5 M NaCl, indicating RNA-dependent binding. Rapamycin/FK506 treatment causes residual release, suggesting some interactions also involve the PPIase cavity.\",\n      \"method\": \"Anti-FKBP25 immunoprecipitation, proteomics, polyribosome fractionation, RNA/salt dissociation experiments\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple interaction partners identified by proteomics with functional dissociation experiments\",\n      \"pmids\": [\"24998444\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"The NMR solution structure of full-length human FKBP25 reveals that the N-terminal helix-loop-helix (HLH) domain and C-terminal FKBD interact with each other. Both domains contribute to DNA binding: the HLH domain makes major-groove contacts, while the basic FKBD loop cooperates with adjacent minor-groove interactions. Mutational studies validated this model.\",\n      \"method\": \"NMR solution structure determination, mutational studies, DNA-binding assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — full-length NMR structure with mutagenesis validation of DNA binding mechanism\",\n      \"pmids\": [\"26762975\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Crystal structure of the ternary complex FRB-rapamycin-FKBP25 was determined at 1.67-Å resolution, revealing rapamycin-induced physical interaction between FKBP25 and the FRB domain of mTOR. Conformational changes in FRB create a methionine-rich hole and covalent metalloid coordination at C2085 of FRB was observed.\",\n      \"method\": \"Proximity biotin-labeling (pBirA), immunoprecipitation, immunofluorescence, X-ray crystallography (1.67 Å)\",\n      \"journal\": \"ACS central science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure of ternary complex plus orthogonal proximity labeling and Co-IP validation\",\n      \"pmids\": [\"27610411\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Mutagenesis of the FKBP25 catalytic domain distinguishes domain-destabilizing mutations from 'surgical' mutations that ablate PPIase activity while maintaining domain fold, providing tools to differentiate catalytic versus non-catalytic functions.\",\n      \"method\": \"Site-directed mutagenesis, in vitro PPIase activity assay, domain folding assessment\",\n      \"journal\": \"Biochemical Society transactions\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 — in vitro mutagenesis and functional characterization, single lab review/methods paper\",\n      \"pmids\": [\"23697935\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"FKBP25 promotes cell proliferation in non-small cell lung cancer through a Sp1/HDAC2/p27 axis: FKBP3 inhibits ubiquitination of the transcription factor Sp1, stabilizing it to drive HDAC2 promoter activity; HDAC2 then modulates histone H3K4 acetylation at the p27 promoter to suppress p27 expression.\",\n      \"method\": \"siRNA knockdown, overexpression, ChIP, luciferase reporter assay, ubiquitination assay, xenograft in vivo model\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (ChIP, reporter, ubiquitination assay) in a single lab\",\n      \"pmids\": [\"28839465\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The N-terminal BTHB domain of FKBP25 specifically binds double-stranded RNA (dsRNA) over single-stranded RNA or DNA. This RNA-binding activity is required for FKBP25 nucleolar localization and for the vast majority of its protein interactions including those with 60S pre-ribosome and early ribosome biogenesis factors. The BTHB and FKBP domains have independent mobility, suggesting the N-terminus anchors to dsRNA while the catalytic domain interacts with neighboring proteins.\",\n      \"method\": \"NMR spectroscopy, RNA binding assays (EMSA and fluorescence), mutagenesis, nucleolar localization imaging, proteomic interaction mapping\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — NMR structural data, mutagenesis, and multiple orthogonal assays confirming dsRNA-binding and functional localization consequence\",\n      \"pmids\": [\"29036638\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"FKBP25 directly binds microtubules via its catalytic FKBP domain to promote microtubule polymerization and stabilize the MT network. FKBP25 associates with the mitotic spindle and regulates entry into mitosis. Depletion leads to increased chromosome instability. Additionally, Protein Kinase C phosphorylates FKBP25 to disrupt its chromatin association during mitosis while maintaining spindle interaction.\",\n      \"method\": \"In vitro microtubule binding and polymerization assay, live cell imaging, knockdown with chromosome instability readout, PKC phosphorylation assay, domain mapping\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — direct in vitro MT binding/polymerization assay, live cell imaging of spindle association, PKC phosphorylation with defined functional consequence\",\n      \"pmids\": [\"29361176\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"FKBP25 promotes homologous recombination (HR) and suppresses single-strand annealing (SSA) in DNA double-strand break repair. Depletion reduces Rad51 repair foci after etoposide and ionizing radiation. The PPIase catalytic activity of FKBP25 is required for this HR-promoting function. Rapamycin impairs HR at least partly independently of mTOR.\",\n      \"method\": \"siRNA knockdown, DSB repair reporter assays, Rad51 foci imaging, rapamycin treatment, catalytic mutant rescue experiments\",\n      \"journal\": \"Biochemistry and cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal DSB repair assays with catalytic mutant demonstrating requirement for enzymatic activity\",\n      \"pmids\": [\"30620620\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"FKBP25 interacts with TRPC6 and regulates non-capacitative calcium entry (NCCE) in platelets and HEK-293 cells. FK506 modifies the association pattern between FKBP25 and TRPC channels. siRNA silencing of FKBP25 inhibits OAG-evoked NCCE, and FKBP25 is found at the plasma membrane by biotinylation experiments.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, calcium flux assay, biotinylation/surface protein isolation, TRPC6-/- mouse platelets\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP interaction plus functional knockdown phenotype with knockout mouse validation, single lab\",\n      \"pmids\": [\"26239116\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"FKBP3 promotes HIV-1 latency by binding to YY1 (indirect association with the HIV-1 LTR) and recruiting HDAC1/2 to the viral LTR, inducing histone deacetylation. FKBP3 knockout in latently infected cell lines promotes latent HIV-1 activation.\",\n      \"method\": \"CRISPR knockout in latent HIV-1 cell lines, co-immunoprecipitation (FKBP3-YY1), ChIP (HDAC1/2 at LTR), latent HIV-1 reactivation assays, primary latent cell model\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP and ChIP with CRISPR KO functional validation, single lab\",\n      \"pmids\": [\"34281390\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ESD (esterase D) interacts with FKBP25 via the FKBP25 N-terminus (1-90 aa), reduces K48-linked polyubiquitination of FKBP25 thereby stabilizing cytoplasmic FKBP25, and promotes FKBP25 binding to mTORC1, suppressing mTORC1 activity and inducing autophagy.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, ubiquitination assay (K48 linkage-specific), mTORC1 substrate phosphorylation (P70S6K, 4EBP1), autophagy assay\",\n      \"journal\": \"Cellular & molecular biology letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — yeast two-hybrid plus Co-IP with functional mTORC1 suppression readout, single lab\",\n      \"pmids\": [\"34875997\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"FKBP25 translocates to the nucleus under ischemic (OGD) or peroxynitrite stress conditions in endothelial cells, where it interacts with 60S ribosomal protein L7a. FKBP25 overexpression protects endothelial cells against OGD injury.\",\n      \"method\": \"Western blot, immunofluorescence, co-immunoprecipitation, FRET, overexpression rescue assay\",\n      \"journal\": \"Cellular physiology and biochemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single Co-IP/FRET interaction with limited mechanistic follow-up, single lab\",\n      \"pmids\": [\"29969783\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"FKBP25 depletion in mouse oocytes causes abnormal spindle assembly, chromosome misalignment, and defective kinetochore-microtubule attachment, leading to elevated aneuploidy. Serine 163 is identified as a major phosphorylation site modulating FKBP25 function in meiotic maturation.\",\n      \"method\": \"siRNA knockdown in mouse oocytes, immunofluorescence (spindle/chromosome), aneuploidy quantification, site-directed mutagenesis (S163A)\",\n      \"journal\": \"Frontiers in cell and developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function with defined spindle/chromosome phenotype plus phospho-site mutagenesis, single lab\",\n      \"pmids\": [\"33553183\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"FKBP3 interacts with PARK7 (DJ-1); FKBP3 knockdown enhances PARK7 ubiquitination and degradation. FKBP3 activates the Wnt/β-catenin signaling pathway through PARK7. FOXO3 binds the FKBP3 promoter to suppress its transcription.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, ChIP (FOXO3 at FKBP3 promoter), Wnt/β-catenin pathway reporters, xenograft model\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP plus ubiquitination assay and ChIP, single lab\",\n      \"pmids\": [\"37987202\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"FKBP25 knockdown in C2C12 myoblasts increases cell viability/accumulation and migration independent of tubulin dynamics, demonstrating a role in myoblast behavior distinct from its previously described microtubule-regulatory function.\",\n      \"method\": \"Doxycycline-inducible shRNA knockdown, cell viability assay, migration assay, tubulin dynamics analysis\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, knockdown with cellular phenotype but no direct molecular mechanism identified\",\n      \"pmids\": [\"37345229\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FKBP25 (encoded by FKBP3) is a nuclear prolyl isomerase with a C-terminal FK506-binding/PPIase domain and an N-terminal Basic Tilted Helix Bundle (BTHB) domain that selectively binds double-stranded RNA to direct nucleolar localization and ribosome biogenesis interactions; the catalytic domain binds microtubules to promote polymerization and spindle integrity, catalytic PPIase activity promotes homologous recombination in DSB repair, chromatin association is cell-cycle regulated by PKC phosphorylation, FKBP25 stabilizes MDM2 auto-ubiquitylation to activate p53, recruits HDAC1/2 via YY1 to repress target loci (including HIV-1 LTR), drives HDAC2 expression through Sp1 stabilization to control cell proliferation, and forms a rapamycin-induced ternary complex with the mTOR FRB domain to modulate mTORC1 signaling.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"FKBP25 (encoded by FKBP3) is a nuclear immunophilin that integrates peptidylprolyl cis-trans isomerase (PPIase) activity with nucleic acid binding to regulate ribosome biogenesis, chromatin dynamics, DNA repair, and mitotic spindle integrity. Its N-terminal Basic Tilted Helix Bundle (BTHB) domain selectively binds double-stranded RNA, which is required for nucleolar localization and association with pre-60S ribosomal subunits and ribosome biogenesis factors, while both the BTHB and C-terminal FKBP domains cooperate to bind DNA [PMID:29036638, PMID:26762975]. The catalytic FKBP domain directly binds microtubules to promote polymerization and spindle stability—with PKC phosphorylation releasing chromatin association during mitosis—and PPIase activity is required for promoting homologous recombination at DNA double-strand breaks [PMID:29361176, PMID:30620620]. FKBP25 also modulates signaling and transcription by stabilizing MDM2 auto-ubiquitylation to activate p53, recruiting HDAC1/2 via YY1 to repress target loci including the HIV-1 LTR, driving HDAC2 expression through Sp1 stabilization, and forming a rapamycin-induced ternary complex with the mTOR FRB domain [PMID:19166840, PMID:34281390, PMID:28839465, PMID:27610411].\",\n  \"teleology\": [\n    {\n      \"year\": 1992,\n      \"claim\": \"Identification of FKBP25 as a nuclear immunophilin with PPIase activity and preferential rapamycin binding established that the FKBP family extends to the nucleus with distinct pharmacological properties.\",\n      \"evidence\": \"Molecular cloning with recombinant PPIase assay and inhibitor IC50 determination\",\n      \"pmids\": [\"1375932\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No in vivo substrates for PPIase activity identified\", \"Nuclear localization signals predicted but not functionally validated\"]\n    },\n    {\n      \"year\": 1993,\n      \"claim\": \"Demonstration that FKBP25 is predominantly nuclear and binds DNA via its unique N-terminal domain distinguished it from cytoplasmic FKBPs and suggested a chromatin-regulatory function.\",\n      \"evidence\": \"Cell fractionation of Jurkat cells, DNA-binding assay, CD spectroscopy\",\n      \"pmids\": [\"8422914\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"DNA-binding specificity (sequence or structure preference) not defined\", \"No mutagenesis to confirm N-terminal domain necessity\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Discovery that FKBP25 stimulates MDM2 auto-ubiquitylation and degradation, thereby activating p53, revealed FKBP25 as a regulator of the p53 tumor-suppressor pathway.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation, siRNA knockdown, ubiquitylation assay\",\n      \"pmids\": [\"19166840\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether PPIase catalytic activity is required for MDM2 interaction not tested\", \"In vivo relevance to tumor suppression not established\", \"Earlier observation that p53 represses FKBP25 transcription (PMID:10557083) suggests a feedback loop whose mechanism is undefined\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Proteomic and structural studies collectively revealed that FKBP25 associates with pre-60S ribosomal subunits in an RNA-dependent manner and that its N-terminal domain adopts a novel BTHB fold, reframing the protein as a ribosome biogenesis factor with a structurally unique nucleic acid-binding module.\",\n      \"evidence\": \"Mass spectrometry interactome, sucrose gradient fractionation, NMR/X-ray crystallography of BTHB domain, RNA/salt dissociation experiments\",\n      \"pmids\": [\"24840943\", \"24667607\", \"24998444\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct substrates of PPIase activity during ribosome maturation unknown\", \"Whether BTHB binds RNA or DNA in vivo was unresolved at this point\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Full-length NMR structure showed both BTHB and FKBP domains cooperate for DNA binding via major- and minor-groove contacts, and the crystal structure of a rapamycin-bridged FRB–FKBP25 ternary complex established a structural basis for rapamycin-dependent mTOR engagement.\",\n      \"evidence\": \"NMR solution structure with mutagenesis validation of DNA contacts; 1.67-Å crystal structure of FRB–rapamycin–FKBP25 plus proximity labeling\",\n      \"pmids\": [\"26762975\", \"27610411\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological significance of FKBP25–mTOR interaction without exogenous rapamycin unclear\", \"Genomic targets of FKBP25 DNA binding not mapped\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"The BTHB domain was shown to be a dsRNA-specific binder whose RNA-binding activity directs nucleolar localization and mediates nearly all protein interactions, resolving the question of whether the N-terminus primarily engages DNA or RNA in vivo.\",\n      \"evidence\": \"NMR, EMSA and fluorescence RNA-binding assays, mutagenesis, nucleolar imaging, proteomic interaction mapping\",\n      \"pmids\": [\"29036638\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific dsRNA targets in the nucleolus not identified\", \"Relative contribution of DNA- versus RNA-binding to chromatin functions unresolved\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"FKBP25 was shown to promote NSCLC cell proliferation through a Sp1/HDAC2/p27 axis, where it stabilizes Sp1 to drive HDAC2 transcription and epigenetically silence the cell-cycle inhibitor p27.\",\n      \"evidence\": \"siRNA/overexpression, ChIP, luciferase reporter, ubiquitination assay, xenograft model\",\n      \"pmids\": [\"28839465\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether PPIase activity is required for Sp1 stabilization not tested\", \"Generalizability beyond NSCLC cell lines unclear\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"The catalytic FKBP domain was found to directly bind microtubules and promote polymerization, while PKC phosphorylation releases FKBP25 from chromatin during mitosis, establishing a dual nuclear/cytoskeletal role regulated by cell-cycle-dependent phosphorylation.\",\n      \"evidence\": \"In vitro MT binding/polymerization, live cell spindle imaging, PKC phosphorylation assay, chromosome instability quantification upon depletion\",\n      \"pmids\": [\"29361176\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of PKC isoform(s) responsible not determined\", \"Structural basis for FKBP domain–tubulin interaction unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"PPIase catalytic activity was directly demonstrated to be required for promoting homologous recombination and Rad51 focus formation at DSBs, establishing an enzymatic role in the DNA damage response.\",\n      \"evidence\": \"DSB repair reporter assays, Rad51 foci imaging, catalytic-dead mutant rescue experiments\",\n      \"pmids\": [\"30620620\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct proline-isomerization substrate in the HR pathway not identified\", \"Rapamycin's HR-inhibitory effect was only partially mTOR-independent, leaving the mechanism unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"FKBP25 was shown to recruit HDAC1/2 to the HIV-1 LTR via YY1 interaction, maintaining viral latency, while oocyte studies confirmed spindle and kinetochore-microtubule functions with identification of S163 as a regulatory phosphosite, and ESD was found to stabilize cytoplasmic FKBP25 to suppress mTORC1.\",\n      \"evidence\": \"CRISPR KO in latent HIV-1 cells with ChIP (PMID:34281390); siRNA in mouse oocytes with aneuploidy quantification and S163A mutagenesis (PMID:33553183); yeast two-hybrid/Co-IP with mTORC1 substrate phosphorylation readout (PMID:34875997)\",\n      \"pmids\": [\"34281390\", \"33553183\", \"34875997\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether FKBP25 isomerase activity is needed for YY1-HDAC recruitment unknown\", \"How ESD-mediated stabilization relates to nuclear FKBP25 functions unaddressed\", \"Direct FKBP25 phosphosite(s) for PKC versus the S163 site relationship not clarified\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"FKBP25 was linked to Wnt/β-catenin signaling through stabilization of PARK7/DJ-1, with FOXO3 acting as a transcriptional repressor of FKBP3, expanding its regulatory network.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, ChIP of FOXO3 at FKBP3 promoter, Wnt reporter, xenograft model\",\n      \"pmids\": [\"37987202\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether PPIase activity mediates PARK7 stabilization untested\", \"Relationship of PARK7-Wnt axis to FKBP25's nuclear and ribosomal functions unclear\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct in vivo substrates of FKBP25 PPIase activity across its diverse functions (HR repair, ribosome biogenesis, chromatin regulation, microtubule dynamics) remain unidentified, and the relative physiological importance of its DNA- versus dsRNA-binding modes is unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No proline-isomerization substrate identified in any pathway\", \"Genome-wide binding profiles (ChIP-seq/CLIP-seq) not reported\", \"No genetic mouse model phenotype characterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 9, 13]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [11]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [1, 7]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [12]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3, 10, 16]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 1, 7, 12]},\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [4, 11]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [12, 18]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [16]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [13]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [12, 18]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [4, 11]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [8, 16]},\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [10, 15]}\n    ],\n    \"complexes\": [\n      \"FRB-rapamycin-FKBP25 ternary complex\",\n      \"YY1-FKBP25-HDAC1/2 repressor complex\",\n      \"pre-60S ribosomal subunit\"\n    ],\n    \"partners\": [\n      \"MDM2\",\n      \"YY1\",\n      \"HDAC1\",\n      \"HDAC2\",\n      \"NCL\",\n      \"TRPC6\",\n      \"ESD\",\n      \"PARK7\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}