Affinage

KLHL15

Kelch-like protein 15 · UniProt Q96M94

Length
604 aa
Mass
69.8 kDa
Annotated
2026-06-10
18 papers in source corpus 9 papers cited in narrative 9 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

KLHL15 functions as a substrate-recognition adaptor for Cullin3 (Cul3)-based E3 ubiquitin ligase complexes, coupling specific substrates to ubiquitination and proteasomal degradation (PMID:23135275). It recognizes substrates through a conserved FRY tripeptide degron, a motif first defined on CtIP and subsequently confirmed on the neuronal microtubule-associated proteins DCX, DCLK1, and DCLK2, where mutation of the FRY motif abolishes KLHL15-dependent ubiquitination and turnover (PMID:27561354, PMID:33199366). Through this activity KLHL15 regulates distinct cellular programs: by degrading CtIP it restrains DNA-end resection and shifts the balance between homologous recombination and non-homologous end-joining (PMID:27561354), while by degrading the doublecortin-family proteins it limits dendritic complexity in hippocampal neurons in a FRY-motif-dependent manner (PMID:33199366). KLHL15 also targets the PP2A regulatory subunit B'β for degradation via a divergent N-terminal recognition element, selectively removing B'β from the PP2A heterotrimer to promote regulatory-subunit exchange (PMID:23135275). The KLHL15-CtIP interaction is a regulated node: the micropeptide PACMP and the cofactor VGLL3 each compete for binding to KLHL15, protecting CtIP from degradation and thereby sustaining the DNA damage response and homologous recombination (PMID:35219381, PMID:39383226).

Mechanistic history

Synthesis pass · year-by-year structured walk · 8 steps
  1. 2005 Low

    Establishing the basic identity of KLHL15 was the prerequisite for any functional study: it was defined as a BTB/POZ- and Kelch-domain protein, the architecture later shown to underlie its adaptor role.

    Evidence in silico cDNA assembly and domain prediction with cross-species sequence comparison

    PMID:15870933

    Open questions at the time
    • Computational only with no functional assay
    • No substrate or ligase partner identified
    • Subcellular localization not determined
  2. 2012 High

    The first functional question — whether KLHL15 is an active E3 adaptor and what it targets — was answered by showing it bridges Cul3 to the PP2A subunit B'β for degradation, establishing both its mechanism and a role in PP2A subunit exchange.

    Evidence proteomic Co-IP/MS, reciprocal Co-IP, in vitro ubiquitylation and degradation assays, mutagenesis of both adaptor and substrate

    PMID:23135275

    Open questions at the time
    • Recognition element on B'β is divergent, not yet generalized to a shared degron
    • Physiological consequence of B'β removal on PP2A signaling not measured
    • No structural data on the adaptor-substrate interface
  3. 2016 High

    Identification of CtIP as a substrate via a conserved FRY tripeptide defined a generalizable degron and linked KLHL15 to control of DNA-end resection and HR/NHEJ choice.

    Evidence reciprocal Co-IP, in vitro ubiquitination, FRY-motif mutagenesis, KLHL15 gain/loss-of-function, HR/NHEJ resection reporter assays

    PMID:27561354

    Open questions at the time
    • Upstream signals controlling KLHL15-CtIP engagement not defined
    • No structural model of FRY recognition
    • Cell-cycle regulation of the interaction unresolved
  4. 2020 High

    Extending the FRY-degron logic to DCX, DCLK1, and DCLK2 showed KLHL15 governs a neuronal substrate class and influences dendritogenesis, demonstrating the adaptor operates across distinct biological contexts.

    Evidence bioinformatic substrate prediction, Co-IP, ubiquitination and half-life assays, FRY mutagenesis, KLHL15 knockdown, dendritic morphology in hippocampal neurons

    PMID:33199366

    Open questions at the time
    • In vivo requirement for KLHL15 in neuronal development not tested
    • Which DCX-family member dominates the dendritic phenotype unclear
    • Regulation of KLHL15 activity in neurons unknown
  5. 2021 Low

    A genetic screen placed KLHL15 in the ATM-inhibitor response, showing its loss protects cells from ATMi-induced damage and implicating it as a modifier of DDR drug sensitivity.

    Evidence genome-wide CRISPR loss-of-function screen under ATM inhibition with viability readout

    PMID:34320214

    Open questions at the time
    • Molecular mechanism of protection not established
    • Not linked directly to CtIP degradation in this study
    • Single screening modality without orthogonal validation
  6. 2022 Medium

    Discovery that the micropeptide PACMP competitively blocks the CtIP-KLHL15 interaction revealed the adaptor's substrate engagement is actively regulated, with therapeutic synthetic-lethality implications.

    Evidence Co-IP of PACMP-KLHL15 and CtIP-KLHL15, ubiquitination and CtIP stability assays, synthetic lethality with PARP inhibition

    PMID:35219381

    Open questions at the time
    • Single-lab mechanism for PACMP competition
    • Structural basis of competitive binding unresolved
    • Whether PACMP affects other KLHL15 substrates untested
  7. 2023 Medium

    Systematic screening and degron mapping placed Cul3-KLHL15 within defined E3-substrate pathways, while structural modeling of a disease-associated Kelch-domain variant pinpointed substrate-binding-surface residues including Tyr552.

    Evidence multiplex pooled CRISPR screens with site-saturation degron mutagenesis; comparative structural modeling of the p.(Arg532del) variant

    PMID:37059329 PMID:37735597

    Open questions at the time
    • Specific substrate identities from the screen not detailed
    • Variant's predicted binding defect not experimentally validated
    • Functional consequence of the variant not established
  8. 2024 Medium

    Identification of VGLL3 as a second competitive protector of CtIP confirmed that multiple factors converge on the KLHL15-CtIP interface to tune HR capacity.

    Evidence Co-IP of VGLL3-KLHL15 and VGLL3-CtIP, competitive binding assays, CtIP stability and HR efficiency assays

    PMID:39383226

    Open questions at the time
    • Single-lab competition mechanism
    • Relationship between VGLL3 and PACMP regulation not reconciled
    • No structural definition of the competing interface

Open questions

Synthesis pass · forward-looking unresolved questions
  • How KLHL15 substrate selection and adaptor activity are regulated across cell-cycle and tissue contexts, and the structural basis of FRY-degron recognition, remain open.
  • No experimental structure of KLHL15 bound to a FRY degron
  • Signals that activate or inhibit KLHL15 in vivo undefined
  • Disease relevance of KLHL15 variants not functionally validated

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 3 GO:0140096 catalytic activity, acting on a protein 3 GO:0016874 ligase activity 2
Pathway
R-HSA-392499 Metabolism of proteins 3 R-HSA-73894 DNA Repair 1
Partners
CTIPCUL3DCLK1DCLK2DCXPACMPRBM6VGLL3
Complex memberships
Cul3-RING E3 ubiquitin ligase (CRL3)

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2012 KLHL15 acts as a substrate adaptor for Cullin3 (Cul3)-based E3 ubiquitin ligase complexes to specifically target the PP2A regulatory subunit B'β for ubiquitylation and proteasomal degradation. KLHL15 residues critical for homodimerization, Cul3 interaction, and B'β interaction were mapped; the divergent N terminus of B'β (including Tyr-52) was necessary and sufficient for KLHL15-mediated degradation. Although KLHL15 can interact with the PP2A/B'β heterotrimer, it only degrades B'β, promoting exchange with other regulatory subunits. Unbiased proteomic screens (Co-IP/MS), co-immunoprecipitation, ubiquitylation assays, proteasomal degradation assays, mutagenesis of KLHL15 and B'β The Journal of biological chemistry High 23135275
2016 KLHL15 is a Cullin3 E3 ligase substrate adaptor that binds CtIP via a conserved tripeptide motif (FRY) in CtIP and promotes CtIP ubiquitination and proteasomal turnover. Mutation of the FRY motif blocks KLHL15-dependent CtIP ubiquitination and degradation. Overexpression of KLHL15 strongly attenuates DNA-end resection, while cells expressing FRY-mutant CtIP or lacking KLHL15 show amplified resection, shifting the balance between homologous recombination (HR) and non-homologous end-joining (NHEJ). Co-immunoprecipitation, ubiquitination assays, site-directed mutagenesis of CtIP FRY motif, KLHL15 overexpression and knockdown, DNA-end resection assays (HR/NHEJ reporter assays) Nature communications High 27561354
2020 KLHL15 interacts with and ubiquitinates doublecortin (DCX), doublecortin-like kinase 1 (DCLK1), and doublecortin-like kinase 2 (DCLK2) — neuronal microtubule-associated proteins — via a Cul3-based E3 ligase complex, targeting them for proteasomal degradation. The interaction is mapped to the tandem DCX domains; a FRY tripeptide at the C-terminal edge of the second DCX domain is necessary for KLHL15-mediated ubiquitination and degradation. Silencing endogenous KLHL15 markedly stabilizes these proteins and prolongs their half-life. KLHL15 overexpression reduces dendritic complexity of cultured hippocampal neurons in a DCX FRY-motif-dependent manner. Bioinformatics substrate prediction, co-immunoprecipitation, ubiquitination assays, pulse-chase/half-life assays, mutagenesis of DCX FRY motif, KLHL15 knockdown, dendritic morphology analysis in cultured hippocampal neurons The Journal of biological chemistry High 33199366
2022 PACMP (a lncRNA-encoded micropeptide) prevents CtIP from KLHL15-mediated ubiquitination and degradation by inhibiting the CtIP-KLHL15 association, thereby maintaining CtIP abundance and DNA damage response. PACMP inhibition causes synthetic lethality through combined CtIP and PARP inhibition. Co-immunoprecipitation showing PACMP-KLHL15 and CtIP-KLHL15 interactions, ubiquitination assays, CtIP stability measurements upon PACMP depletion, synthetic lethality assays Molecular cell Medium 35219381
2023 Multiplex CRISPR screening identified substrates for the Cul3-KLHL15 E3 ubiquitin ligase and mapped cognate degron motifs through site-saturation mutagenesis, placing KLHL15 within defined E3 ligase-substrate pathways in the ubiquitin-proteasome system. Multiplex CRISPR screening (~100 pooled CRISPR screens), site-saturation mutagenesis, degron mapping Nature cell biology Medium 37735597
2024 VGLL3 protects CtIP from KLHL15-mediated ubiquitination and degradation through competitive binding with KLHL15, thereby maintaining CtIP levels and promoting efficient homologous recombination and DNA double-strand break repair. Co-immunoprecipitation showing VGLL3-KLHL15 and VGLL3-CtIP interactions, competitive binding assays, CtIP stability assays upon VGLL3 depletion, HR efficiency assays Science advances Medium 39383226
2021 CRISPR screen demonstrated that KLHL15 loss protects cells from DNA damage induced by ATM inhibition, placing KLHL15 loss as a genetic modifier of ATM inhibitor sensitivity in the DNA damage response pathway. Genome-wide CRISPR loss-of-function screen with ATM inhibitor treatment, cell viability readout Nucleic acids research Low 34320214
2005 KLHL15 was identified as a novel human Kelch-like protein containing an N-terminal BTB/POZ domain and C-terminal Kelch motifs (three KELCH repeats), encoded by a 4-exon gene on the X chromosome, with ubiquitous mRNA expression across tissues and 85–93% amino acid identity to chicken and zebrafish orthologs. Bioinformatics/in silico analysis, cDNA assembly, domain prediction (Pfam), tissue expression by database analysis Oncology reports Low 15870933
2023 Structural modeling of the KLHL15 p.(Arg532del) variant predicts altered topology at the substrate-binding surface of the Kelch repeat domain, including at Tyr552, which is known to be important for substrate binding, suggesting this residue contributes to the stability of loop regions at the substrate-binding surface. Comparative protein structural modeling of variant vs wild-type KLHL15 Kelch repeat domain European journal of medical genetics Low 37059329

Source papers

Stage 0 corpus · 18 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2015 X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes. Molecular psychiatry 248 25644381
2022 Micropeptide PACMP inhibition elicits synthetic lethal effects by decreasing CtIP and poly(ADP-ribosyl)ation. Molecular cell 77 35219381
2016 Cullin3-KLHL15 ubiquitin ligase mediates CtIP protein turnover to fine-tune DNA-end resection. Nature communications 55 27561354
2023 Defining E3 ligase-substrate relationships through multiplex CRISPR screening. Nature cell biology 53 37735597
2012 Selective proteasomal degradation of the B'β subunit of protein phosphatase 2A by the E3 ubiquitin ligase adaptor Kelch-like 15. The Journal of biological chemistry 36 23135275
2014 Intragenic rearrangements in X-linked intellectual deficiency: results of a-CGH in a series of 54 patients and identification of TRPC5 and KLHL15 as potential XLID genes. American journal of medical genetics. Part A 28 24817631
2021 Genetic vulnerabilities upon inhibition of DNA damage response. Nucleic acids research 26 34320214
2019 Integrated Analysis of lncRNA and mRNA Transcriptomes Reveals New Regulators of Ubiquitination and the Immune Response in Silica-Induced Pulmonary Fibrosis. BioMed research international 15 30756084
2020 The X-linked intellectual disability gene product and E3 ubiquitin ligase KLHL15 degrades doublecortin proteins to constrain neuronal dendritogenesis. The Journal of biological chemistry 12 33199366
2020 Identification of Differentially Expressed Gene Transcripts in Porcine Endometrium during Early Stages of Pregnancy. Life (Basel, Switzerland) 10 32429378
2024 VGLL3 modulates chemosensitivity through promoting DNA double-strand break repair. Science advances 7 39383226
2005 Identification and characterization of a novel kelch-like gene KLHL15 in silico. Oncology reports 7 15870933
2021 Integrated analysis of ceRNA network and tumor-infiltrating immune cells in esophageal cancer. Bioscience reports 5 33960364
2023 Clinical findings and structural analysis involving a patient with a novel KLHL15 variant. European journal of medical genetics 1 37059329
2023 X-linked intellectual disability related to a novel variant of KLHL15. Human genome variation 1 37452054
2026 Variants in KLHL15, encoding a regulator of protein ubiquitination, linked to focal epilepsy with neurodevelopmental disorders. Seizure 0 42097059
2025 Identification of characteristic genes ofanddeficiency constitutions: an integrated analysis based on bioinformatics and machine learning. Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan 0 40810238
2024 [Clinical features and genetic analysis of 17 Chinese pedigrees affected with X-linked intellectual disability]. Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics 0 38684296

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