Affinage

KLHL13

Kelch-like protein 13 · UniProt Q9P2N7

Length
655 aa
Mass
73.9 kDa
Annotated
2026-04-28
19 papers in source corpus 12 papers cited in narrative 12 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

KLHL13 is a BTB-Kelch family substrate adaptor for the CUL3 RING E3 ubiquitin ligase that directs ubiquitination of multiple substrates to control mitotic progression, signal transduction, and organelle homeostasis. Together with KLHL9, KLHL13 forms a heteromeric adaptor complex with CUL3 that directly binds and ubiquitinates Aurora B kinase, removing it from mitotic chromosomes to enable proper chromosome alignment, midzone formation, cytokinesis, and spindle assembly checkpoint maintenance (PMID:17543862, PMID:18075312, PMID:19995937). Beyond Aurora B, the KLHL9/KLHL13/CUL3 complex ubiquitinates IRS1 to attenuate insulin signaling (PMID:31515271), catalyzes K63-linked ubiquitination of IMMT to initiate SQSTM1-dependent mitophagy (PMID:38834545), ubiquitinates TAP2 to impair antigen presentation (PMID:41315272), and targets CEP57L1 for degradation to control centrosome number (PMID:41443421). Loss-of-function variants in the X-linked KLHL13 gene cause a neurodevelopmental disorder characterized by genomic instability, and the associated cellular and neurobehavioral deficits are rescued by Aurora B kinase inhibition, establishing AURKB dysregulation as the pathogenic mechanism (PMID:41159445).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2007 High

    Establishing that KLHL13 functions as a substrate-specific adaptor in a CUL3 E3 ligase complex that directly ubiquitinates Aurora B resolved how the chromosomal passenger complex is removed from chromosomes during anaphase, linking a BTB-Kelch protein to mitotic progression and cytokinesis.

    Evidence In vitro reconstituted ubiquitylation, direct binding assays, co-immunoprecipitation, siRNA knockdown with mitotic phenotype readout in human cells

    PMID:17543862

    Open questions at the time
    • Structural basis of Aurora B recognition by the KLHL13 Kelch domain not determined
    • Whether KLHL13 and KLHL9 form obligate heterodimers or function independently unclear
    • In vivo validation in animal models lacking
  2. 2007 Medium

    Demonstrating that CUL3/KLHL9/KLHL13 inactivation causes premature Cyclin B degradation and spindle checkpoint failure extended the complex's mitotic role beyond Aurora B relocalization to checkpoint signaling integrity.

    Evidence siRNA knockdown of KLHL9/KLHL13/CUL3 with Cyclin B monitoring and SAC activity assays

    PMID:18075312

    Open questions at the time
    • Whether SAC defect is a direct consequence of Aurora B mislocalization or involves additional substrates not resolved
    • Independent replication by other groups not reported at the time
  3. 2009 High

    Showing that KLHL13 (with KLHL9) regulates a chromosomal pool of Aurora B distinct from the midzone pool controlled by KLHL21 established that CUL3 employs non-redundant BTB-Kelch adaptors for spatially compartmentalized ubiquitination of the same substrate.

    Evidence Immunofluorescence localization and in vitro ubiquitination comparing KLHL13 and KLHL21 complexes

    PMID:19995937

    Open questions at the time
    • Mechanism determining spatial specificity of KLHL13 vs. KLHL21 not elucidated
    • How KLHL9/KLHL13 are themselves recruited to chromosomes unknown
  4. 2017 Medium

    The finding that SCCRO-dependent neddylation activates CUL3-KLHL21 but not CUL3-KLHL9/KLHL13 revealed that distinct regulatory inputs control different CUL3 adaptor complexes despite sharing the same cullin scaffold.

    Evidence SCCRO knockout/knockdown with functional assays for CUL3 complex activity and neddylation

    PMID:28620047

    Open questions at the time
    • The neddylation mechanism that does activate the KLHL9/KLHL13 complex not identified
    • Structural basis of selective neddylation unknown
  5. 2019 High

    Identification of IRS1 as a KLHL13/CUL3 substrate expanded the complex's function beyond mitosis into metabolic signaling, showing it promotes IRS1 proteasomal degradation and thereby attenuates insulin signaling.

    Evidence BioID proximity labeling, co-immunoprecipitation, siRNA knockdown restoring IRS1 levels and insulin signaling in ATG16L1-deficient cells

    PMID:31515271

    Open questions at the time
    • Direct ubiquitination of IRS1 by reconstituted KLHL13/CUL3 complex not shown in vitro
    • IRS1 ubiquitination site(s) not mapped
    • Physiological role in whole-organism insulin sensitivity not tested
  6. 2021 Medium

    A chromosome-wide CRISPR screen in murine ESCs revealed that KLHL13 promotes pluripotency factor expression and delays differentiation, positioning it as a mediator of X-chromosome dosage effects on stem cell identity.

    Evidence CRISPR knockout screen with pluripotency, MAPK signaling, and differentiation readouts in mESCs

    PMID:33863351

    Open questions at the time
    • Substrate(s) through which KLHL13 modulates MAPK target gene repression not identified
    • Whether this role requires CUL3 or KLHL9 not tested
    • Relevance to human ESC biology not established
  7. 2024 High

    Discovery that the KLHL9/KLHL13/CUL3 complex catalyzes K63-linked ubiquitination of IMMT at K211 to initiate SQSTM1-mediated mitophagy demonstrated the complex can generate non-degradative ubiquitin chains and regulate organelle quality control, a function co-opted by the bacterial pathogen Burkholderia pseudomallei.

    Evidence Ubiquitome profiling, co-immunoprecipitation, site-directed mutagenesis of IMMT K211, mitophagy and ROS assays

    PMID:38834545 PMID:39265641

    Open questions at the time
    • Whether KLHL13/CUL3-dependent mitophagy occurs under physiological (non-infection) conditions not shown
    • Chain-type specificity determinants within the complex not resolved
  8. 2025 Medium

    Identification of TAP2, CEP57L1, and the E2 UBE2D3 as components of KLHL13-dependent ubiquitination pathways broadened the substrate repertoire to antigen presentation and centrosome duplication control, while RHOBTB2 was identified as a stabilizer of KLHL13 protein.

    Evidence Co-immunoprecipitation, site-directed mutagenesis (TAP2 K245), siRNA/overexpression (CEP57L1), proteasome inhibitor experiments (RHOBTB2-KLHL13 axis)

    PMID:41107424 PMID:41315272 PMID:41443421

    Open questions at the time
    • TAP2 and CEP57L1 ubiquitination by reconstituted KLHL13/CUL3 complex not demonstrated in vitro
    • Whether RHOBTB2-mediated stabilization of KLHL13 is direct or through an intermediary not fully resolved
    • Each substrate identified in a single study
  9. 2025 High

    Human genetic evidence established that loss-of-function KLHL13 variants cause an X-linked neurodevelopmental disorder, and pharmacologic rescue by Aurora B inhibition in cells and zebrafish proved that AURKB dysregulation is the disease mechanism.

    Evidence Exome sequencing of affected families, overexpression of patient variants in HEK293T, zebrafish klhl13 knockdown with mRNA rescue, AZD1152-HQPA rescue of genomic instability and neurobehavioral deficits

    PMID:41159445

    Open questions at the time
    • Mouse knockout model not reported
    • Tissue-specific requirements (e.g. neuronal vs. progenitor) not delineated
    • Whether other substrates contribute to neurodevelopmental pathology not excluded

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key open questions include the structural basis for KLHL13 substrate selectivity, the determinants of K48- vs. K63-linked chain assembly by the same adaptor complex, whether KLHL9 is an obligate partner for all substrates, and the in vivo relevance of non-Aurora B substrates to KLHL13-associated disease.
  • No crystal or cryo-EM structure of KLHL13 or its CUL3 complex available
  • Mechanism selecting K48 vs. K63 chain type not known
  • Relative contribution of each substrate to neurodevelopmental phenotype untested

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
Localization
GO:0005694 chromosome 2 GO:0005829 cytosol 2
Pathway
R-HSA-392499 Metabolism of proteins 5 R-HSA-1640170 Cell Cycle 4 R-HSA-9612973 Autophagy 2 R-HSA-1643685 Disease 1
Partners
AURKBCEP57L1CUL3IMMTIRS1KLHL9RHOBTB2UBE2D3
Complex memberships
CUL3/KLHL9/KLHL13 E3 ubiquitin ligase complex

Evidence

Reading pass · 12 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2007 KLHL13 acts as a substrate-specific adaptor for a Cul3-based E3 ubiquitin ligase complex (Cul3/KLHL9/KLHL13). Aurora B directly binds to the substrate-recognition domain of KLHL13 in vitro, is coimmunoprecipitated with the Cul3 complex during mitosis, and is ubiquitylated by reconstituted Cul3/KLHL9/KLHL13 ligase in vitro. This complex removes Aurora B (chromosomal passenger complex) from mitotic chromosomes, allowing accumulation on the central spindle during anaphase, and is required for correct chromosome alignment, midzone/midbody formation, and cytokinesis. In vitro binding assay, co-immunoprecipitation, in vitro ubiquitylation reconstitution, siRNA knockdown with mitotic phenotype readout Developmental cell High 17543862
2007 Inactivation of the Cul3/KLHL9/KLHL13 ligase leads to premature degradation of Cyclin B and premature exit from the mitotic state in the presence of microtubule poisons, indicating a role for this complex in maintaining spindle assembly checkpoint (SAC) signaling. siRNA knockdown of KLHL9/KLHL13/Cul3 with Cyclin B protein level monitoring and SAC activity assay Cell cycle (Georgetown, Tex.) Medium 18075312
2009 KLHL13 (together with KLHL9), unlike KLHL21, does not localize to midzone microtubules in anaphase; the Cul3/KLHL9/KLHL13 complex regulates a distinct chromosomal pool of Aurora B compared to Cul3/KLHL21, demonstrating non-redundant spatial regulation of Aurora B ubiquitination during mitosis. Immunofluorescence localization, siRNA knockdown, in vitro ubiquitination assay The Journal of cell biology High 19995937
2017 The activity of the Cul3/KLHL9/KLHL13 complex is intact in SCCRO-deficient cells, demonstrating that SCCRO selectively neddylates Cul3 in the context of KLHL21 but not KLHL9/KLHL13, and that KLHL9/KLHL13 and KLHL21 are distinct Cul3 adaptor complexes regulated by different neddylation mechanisms. Loss-of-function (SCCRO KO/KD), functional assays for Cul3 complex activity, neddylation assays The Journal of biological chemistry Medium 28620047
2019 KLHL13 (together with KLHL9) forms an E3 ubiquitin ligase complex with CUL3 that promotes proteasomal degradation of IRS1, a key insulin signaling scaffold. KLHL9 and KLHL13 were identified as novel IRS1 interactors by BioID proximity labeling and co-immunoprecipitation. siRNA knockdown of Klhl13 or Cul3 recovered IRS1 expression and restored insulin signaling in ATG16L1-deficient cells. BioID proximity-dependent biotinylation, co-immunoprecipitation, siRNA knockdown with IRS1 protein level and insulin signaling readout The Journal of biological chemistry High 31515271
2021 KLHL13 is an X-linked gene that promotes pluripotency factor expression and delays differentiation in murine embryonic stem cells by acting downstream in the female pluripotency phenotype pathway, while Dusp9 affects MAPK pathway intermediates; both jointly repress MAPK target gene expression. Chromosome-wide CRISPR knockout screen, secondary screens assaying pluripotency factor expression, MAPK signaling, and differentiation timing Genome biology Medium 33863351
2024 The KLHL9/KLHL13/CUL3 E3 ubiquitin ligase complex ubiquitinates the inner mitochondrial membrane protein IMMT at K211 with K63-linked chains during Burkholderia pseudomallei infection (mediated by the bacterial effector BipD which binds the Back and Kelch domains of KLHL9/KLHL13). This K63-linked ubiquitination of IMMT initiates mitophagy via the SQSTM1 receptor pathway, reducing mitochondrial ROS production and facilitating bacterial survival. Co-immunoprecipitation, ubiquitome profiling (host ubiquitome), site-directed mutagenesis of IMMT K211, mitophagy assay, ROS measurement Nature communications High 38834545
2024 KLHL13 participates in K63-linked ubiquitination of IMMT/mitofilin at K211 as part of the KLHL9-KLHL13-CUL3 E3 ubiquitin ligase complex, initiating mitophagy through the conventional macroautophagy pathway involving SQSTM1. Mechanistic follow-up study: co-immunoprecipitation, ubiquitination site mutagenesis, mitophagy pathway characterization Autophagy High 39265641
2025 UBE2D3 binds KLHL13 and mediates K63-linked polyubiquitination at lysine 245 of TAP2, causing steric hindrance that blocks the TAP2 transporter and impairing antigen presentation in pancreatic cancer. Inhibition of UBE2D3 restores antigen presentation and CD8+ T-cell-mediated tumor surveillance. Co-immunoprecipitation, site-directed mutagenesis (K245 of TAP2), antigen presentation assay, genetic/pharmacologic inhibition with CD8+ T-cell functional readout Nature communications Medium 41315272
2025 RHOBTB2 directly interacts with KLHL13 (validated by co-immunoprecipitation) and stabilizes KLHL13 protein by inhibiting its proteasomal degradation. RHOBTB2 overexpression upregulates KLHL13 protein levels, and this stabilization is reversed by the proteasome inhibitor MG132, placing KLHL13 downstream of RHOBTB2 in the Hippo-YAP1 signaling pathway in AML cells. Co-immunoprecipitation, Western blot with/without proteasome inhibitor MG132, siRNA knockdown, overexpression functional assays Scientific reports Medium 41107424
2025 KLHL13 functional defects (frameshift and missense variants found in patients with X-linked neurodevelopmental disorder) impair KLHL13-mediated cell-cycle regulation during mitosis, leading to genomic instability. Overexpression of NDD-associated KLHL13 variants in HEK293T cells disrupted mitotic cell-cycle regulation. Knockdown of klhl13 in zebrafish caused developmental deficits rescued by wild-type human KLHL13 mRNA but not NDD-variant transcripts. Treatment with Aurora B kinase inhibitor AZD1152-HQPA rescued genomic instability in cells and neurobehavioral deficits in zebrafish, confirming that KLHL13 acts through AURKB regulation. Exome sequencing, in silico protein modeling, overexpression of variants in HEK293T cells, zebrafish klhl13 knockdown, mRNA rescue, Aurora B inhibitor rescue experiments Genetics in medicine : official journal of the American College of Medical Genetics High 41159445
2025 In colorectal cancer cells, KLF5-mediated transcription of KLHL13 and CUL3 is required for proteasomal ubiquitination and degradation of CEP57L1. AGE treatment downregulates KLF5, KLHL13, and CUL3, leading to CEP57L1 accumulation and centrosome amplification, which drives cancer cell metastasis. siRNA knockdown, Western blot, overexpression, mouse metastasis model, human cancer tissue cohort The Journal of biological chemistry Medium 41443421

Source papers

Stage 0 corpus · 19 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2007 A Cul3-based E3 ligase removes Aurora B from mitotic chromosomes, regulating mitotic progression and completion of cytokinesis in human cells. Developmental cell 196 17543862
2009 The Cul3-KLHL21 E3 ubiquitin ligase targets aurora B to midzone microtubules in anaphase and is required for cytokinesis. The Journal of cell biology 118 19995937
2014 Whole-exome sequencing in patients with inherited neuropathies: outcome and challenges. Journal of neurology 61 24627108
2019 A Genome-Wide Knockout Screen in Human Macrophages Identified Host Factors Modulating Salmonella Infection. mBio 43 31594818
2019 Deficiency of the autophagy gene ATG16L1 induces insulin resistance through KLHL9/KLHL13/CUL3-mediated IRS1 degradation. The Journal of biological chemistry 34 31515271
2021 Identification of X-chromosomal genes that drive sex differences in embryonic stem cells through a hierarchical CRISPR screening approach. Genome biology 32 33863351
2022 Integrative RNA profiling of TBEV-infected neurons and astrocytes reveals potential pathogenic effectors. Computational and structural biotechnology journal 30 35685361
2007 A Cul3-based E3 ligase regulates mitosis and is required to maintain the spindle assembly checkpoint in human cells. Cell cycle (Georgetown, Tex.) 20 18075312
2021 Targeting Cul3-scaffold E3 ligase complex via KLHL substrate adaptors for cancer therapy. Pharmacological research 16 33872809
2020 Comparative transcriptome analysis of the hippocampus from sleep-deprived and Alzheimer's disease mice. Genetics and molecular biology 15 32338274
2017 Squamous cell carcinoma-related oncogene (SCCRO) neddylates Cul3 protein to selectively promote midbody localization and activity of Cul3KLHL21 protein complex during abscission. The Journal of biological chemistry 15 28620047
2020 Expression Patterns of Immune Genes Reveal Heterogeneous Subtypes of High-Risk Neuroblastoma. Cancers 14 32629858
2024 Burkholderia pseudomallei BipD modulates host mitophagy to evade killing. Nature communications 11 38834545
2024 Predicting biomarkers related to idiopathic pulmonary fibrosis: Robust ranking aggregation analysis and animal experiment verification. International immunopharmacology 7 39067403
2025 RHOBTB2 enhances cell proliferation of acute myeloid leukemia by modulating Hippo-YAP1 signaling and dependent of KLHL13. Scientific reports 1 41107424
2024 Burkholderia pseudomallei BipD initiates mitophagy to evade killing by hijacking host KLHL9-KLHL13-CUL3 E3 ligase to ubiquitinate IMMT. Autophagy 1 39265641
2025 KLHL13 functional defects cause neurodevelopmental disorder in humans that can be rescued via inhibition of AURKB in cellular and animal models. Genetics in medicine : official journal of the American College of Medical Genetics 0 41159445
2025 IFN-γ-driven UBE2D3 upregulation impairs antigen presentation pathways and anti-tumor immunity in pancreatic cancer. Nature communications 0 41315272
2025 AGEs promote the metastasis of colorectal cancer cells via centrosome amplification by KLF5-CEP57L1 axis. The Journal of biological chemistry 0 41443421