Affinage

KLHL15

Kelch-like protein 15 · UniProt Q96M94

Length
604 aa
Mass
69.8 kDa
Annotated
2026-04-28
17 papers in source corpus 9 papers cited in narrative 9 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

KLHL15 is a substrate adaptor for Cullin3 (Cul3)-based E3 ubiquitin ligase complexes that targets multiple substrates for ubiquitination and proteasomal degradation, thereby controlling DNA damage repair pathway choice, PP2A holoenzyme composition, and neuronal morphogenesis. KLHL15 recognizes substrates through defined degron motifs—a conserved FRY tripeptide in CtIP and doublecortin-family proteins (DCX, DCLK1, DCLK2), and a divergent N-terminal sequence in the PP2A regulatory subunit B'β—and promotes their polyubiquitination via the Cul3 scaffold (PMID:23135275, PMID:27561354, PMID:33199366). KLHL15-mediated degradation of CtIP fine-tunes DNA-end resection and the balance between homologous recombination and non-homologous end-joining, while degradation of DCX-domain proteins restricts dendritic arborization in hippocampal neurons (PMID:27561354, PMID:33199366). Competing interactors including the micropeptide PACMP and VGLL3 antagonize KLHL15 by blocking substrate access, thereby stabilizing CtIP and promoting homologous recombination during the DNA damage response (PMID:35219381, PMID:39383226).

Mechanistic history

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

    Initial identification of KLHL15 as a BTB/Kelch-domain protein established the structural framework predicting it as a candidate Cul3 adaptor, but left its function entirely open.

    Evidence Bioinformatic cDNA assembly, domain prediction, and tissue expression survey

    PMID:15870933

    Open questions at the time
    • No biochemical or functional validation performed
    • No substrates or interactors identified
    • Cul3 binding not tested
  2. 2012 High

    Demonstration that KLHL15 serves as a Cul3 E3 ligase adaptor targeting the PP2A B'β subunit for ubiquitination and degradation established its molecular function, revealing that KLHL15 selectively degrades free B'β but not the assembled PP2A heterotrimer, thereby regulating PP2A regulatory subunit exchange.

    Evidence Co-immunoprecipitation, in vivo and in vitro ubiquitylation assays, domain mapping and mutagenesis of KLHL15 and B'β

    PMID:23135275

    Open questions at the time
    • Physiological consequence of altered PP2A composition not characterized
    • Structural basis of B'β N-terminal recognition by KLHL15 Kelch domain unresolved
    • No in vivo animal model phenotype
  3. 2016 High

    Identification of CtIP as a KLHL15 substrate through a conserved FRY degron motif revealed that KLHL15 controls DNA-end resection and HR/NHEJ pathway choice, expanding its functional scope from phosphatase regulation to DNA repair.

    Evidence Co-IP, ubiquitination assays, FRY motif mutagenesis, KLHL15 overexpression/knockout, DNA-end resection and HR/NHEJ reporter assays

    PMID:27561354

    Open questions at the time
    • Cell-cycle regulation of KLHL15 activity not determined
    • How KLHL15 activity is coordinated with other CtIP E3 ligases unclear
    • No structural data for FRY motif recognition
  4. 2020 High

    Extension of the FRY degron paradigm to doublecortin-family proteins (DCX, DCLK1, DCLK2) demonstrated that KLHL15 controls neuronal dendritogenesis by degrading microtubule-associated proteins, establishing it as a multi-substrate adaptor with roles beyond DNA repair.

    Evidence Bioinformatic substrate prediction, Co-IP, ubiquitination assays, FRY mutagenesis, siRNA knockdown, cycloheximide chase, primary hippocampal neuron morphology analysis

    PMID:33199366

    Open questions at the time
    • In vivo neuronal phenotype of KLHL15 loss not characterized in animal models
    • Relative contribution of DCX vs DCLK substrates to dendritic phenotype unknown
    • Whether KLHL15 regulates neuronal migration through DCX degradation untested
  5. 2021 Medium

    A genome-wide CRISPR screen placed KLHL15 in a genetic interaction network with ATM, showing that KLHL15 loss protects cells from ATM inhibitor-induced DNA damage, consistent with its role in CtIP-dependent resection control.

    Evidence CRISPR loss-of-function screen with ATM inhibitor, cell viability assays

    PMID:34320214

    Open questions at the time
    • Mechanism inferred from prior CtIP literature rather than directly dissected
    • Whether protection acts solely through CtIP stabilization not formally tested
    • Therapeutic relevance of KLHL15 loss in ATMi-treated tumors unexplored
  6. 2022 High

    Discovery that the micropeptide PACMP competitively blocks the CtIP–KLHL15 interaction revealed a novel regulatory layer in which a non-coding RNA-encoded peptide antagonizes Cul3-KLHL15 substrate access to maintain CtIP abundance during DNA damage.

    Evidence Co-IP, ubiquitination assays, PACMP overexpression/knockdown, CtIP stability assays

    PMID:35219381

    Open questions at the time
    • Structural basis of PACMP–KLHL15 competition unknown
    • Whether PACMP also blocks other KLHL15 substrates untested
    • Regulation of PACMP expression during DNA damage incompletely characterized
  7. 2023 Medium

    Multiplex CRISPR screening systematically confirmed KLHL15 degron specificity at scale, validating that defined short sequences encode Cul3-KLHL15 substrate recognition.

    Evidence Multiplex CRISPR screening with site-saturation mutagenesis for degron mapping

    PMID:37735597

    Open questions at the time
    • Full substrate repertoire beyond known targets not individually validated
    • Degron affinity hierarchy among substrates not quantified
    • Screening performed as part of broader platform—KLHL15-specific depth limited
  8. 2024 Medium

    Identification of VGLL3 as a second competitive inhibitor of KLHL15-mediated CtIP degradation established that multiple proteins converge to protect CtIP from Cul3-KLHL15 and promote HR, revealing a regulatory hub at the KLHL15–CtIP interface.

    Evidence Competitive Co-IP, CtIP ubiquitination assays, VGLL3 depletion with HR efficiency measurement

    PMID:39383226

    Open questions at the time
    • Whether VGLL3 and PACMP act redundantly or in distinct contexts not resolved
    • Structural mechanism of competitive binding unclear
    • VGLL3 effects on other KLHL15 substrates not examined

Open questions

Synthesis pass · forward-looking unresolved questions
  • No high-resolution structure of KLHL15 in complex with any substrate or competitor exists, and the in vivo physiological consequences of KLHL15 loss in animal models remain uncharacterized.
  • No crystal or cryo-EM structure of KLHL15 Kelch domain bound to FRY degron or B'β N-terminus
  • No KLHL15 knockout mouse or zebrafish phenotype reported
  • Cell-cycle or DNA-damage-dependent regulation of KLHL15 protein levels or activity unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 6 GO:0060090 molecular adaptor activity 3
Pathway
R-HSA-392499 Metabolism of proteins 4 R-HSA-73894 DNA Repair 4 R-HSA-1266738 Developmental Biology 1
Partners
CTIPCUL3DCLK1DCLK2DCXPPP2R5BRBBP4VGLL3
Complex memberships
CUL3-KLHL15 E3 ubiquitin ligase

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, specifically targeting the PP2A regulatory subunit B'β for ubiquitylation and proteasomal degradation. The divergent N terminus of B'β (including Tyr-52) is necessary and sufficient for KLHL15-mediated degradation. KLHL15 residues critical for homodimerization and interaction with Cul3 and B'β were mapped. Although KLHL15 can interact with the PP2A/B'β heterotrimer, it degrades only free B'β, promoting regulatory subunit exchange. Co-immunoprecipitation, proteomic screens, ubiquitylation assays, proteasomal degradation assays, domain mapping/mutagenesis The Journal of biological chemistry High 23135275
2016 KLHL15 functions as a Cullin3 E3 ligase substrate adaptor that promotes CtIP protein turnover via the ubiquitin-proteasome pathway, thereby fine-tuning DNA-end resection and the balance between homologous recombination (HR) and non-homologous end-joining (NHEJ). A conserved FRY tripeptide motif in CtIP is essential for KLHL15 binding; FRY mutation blocks KLHL15-dependent CtIP ubiquitination and degradation. Overexpression of KLHL15 strongly attenuates DNA-end resection, while KLHL15 loss or FRY-mutant CtIP amplifies resection. Co-immunoprecipitation, ubiquitination assays, site-directed mutagenesis (FRY motif), KLHL15 overexpression and knockout cell lines, DNA-end resection assays, HR/NHEJ reporter assays Nature communications High 27561354
2020 KLHL15 targets doublecortin (DCX) and doublecortin-like kinases 1 and 2 (DCLK1, DCLK2) for ubiquitination and proteasomal degradation via a Cullin3-based E3 ligase complex. Interaction is mediated through 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 stabilizes DCX domain-containing proteins and prolongs their half-life. Functionally, KLHL15 overexpression reduces dendritic complexity of hippocampal neurons in a DCX FRY-dependent manner. Bioinformatics substrate identification, co-immunoprecipitation, ubiquitination assays, domain mapping, site-directed mutagenesis (FRY motif), siRNA knockdown, cycloheximide chase assay, primary neuron morphology analysis The Journal of biological chemistry High 33199366
2022 The micropeptide PACMP (encoded by lncRNA CTD-2256P15.2) inhibits CtIP-KLHL15 association, thereby preventing KLHL15-mediated ubiquitination and degradation of CtIP. This represents a regulatory mechanism where PACMP acts as a decoy to block KLHL15 substrate access and maintain CtIP abundance during DNA damage response. Co-immunoprecipitation, ubiquitination assays, PACMP overexpression/knockdown, CtIP stability assays Molecular cell High 35219381
2023 Multiplex CRISPR screening identified substrates and cognate degron motifs for Cul3KLHL15, demonstrating that KLHL15 substrate specificity is encoded in defined degron sequences recognizable at scale. The platform confirmed KLHL15 as a Cul3 substrate adaptor with definable substrate degrons. Multiplex CRISPR screening, site-saturation mutagenesis for degron mapping Nature cell biology Medium 37735597
2021 KLHL15 loss protects cells from DNA damage induced by ATM inhibition, placing KLHL15 in a genetic interaction network with ATM-dependent DNA damage response, consistent with its role in controlling CtIP levels and DNA-end resection. CRISPR loss-of-function screen with ATM inhibitor, cell viability assays Nucleic acids research Medium 34320214
2024 VGLL3 prevents CtIP from KLHL15-mediated ubiquitination and degradation through competitive binding with KLHL15, thereby stabilizing CtIP and promoting homologous recombination efficiency during DNA damage response. Co-immunoprecipitation (competitive binding assay), CtIP ubiquitination assays, VGLL3 depletion with HR efficiency measurement Science advances Medium 39383226
2005 KLHL15 was identified as a novel human Kelch-like protein containing an N-terminal BTB/POZ domain and C-terminal Kelch motifs, encoded by a 4-exon gene on chromosome X, with ubiquitous mRNA expression across tissues. The protein shows 85-93% amino acid identity across human, chicken, and zebrafish. Bioinformatics/in silico analysis, cDNA assembly, domain prediction (Pfam), tissue expression survey 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 perturbation at Tyr552, a residue known to be important for substrate binding, providing a structural rationale for loss of KLHL15 E3 adaptor function. Comparative structural modelling of variant protein European journal of medical genetics Low 37059329

Source papers

Stage 0 corpus · 17 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 246 25644381
2022 Micropeptide PACMP inhibition elicits synthetic lethal effects by decreasing CtIP and poly(ADP-ribosyl)ation. Molecular cell 76 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 49 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 24 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 11 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
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
2023 X-linked intellectual disability related to a novel variant of KLHL15. Human genome variation 0 37452054