KLHL13

KLHL13 is a BTB-Kelch substrate-recognition adaptor that, together with KLHL9, assembles a CUL3-based E3 ubiquitin ligase governing mitotic progression by directly binding and ubiquitylating Aurora B (AURKB) to extract it from chromosomes and enable chromosomal passenger complex translocation to the central spindle during anaphase, an activity required for chromosome alignment, midbody formation, cytokinesis, and spindle assembly checkpoint maintenance (PMID:17543862, PMID:18075312, PMID:19995937). The Kelch substrate-recognition domain of KLHL13 makes the direct AURKB contact, and the reconstituted CUL3/KLHL9/KLHL13 ligase ubiquitylates AURKB both in vitro and in a CUL3-dependent manner in cells (PMID:17543862). Beyond this mitotic role, the same KLHL9/KLHL13/CUL3 complex targets IRS1 for proteasomal degradation to dampen insulin signaling (PMID:31515271), and is hijacked by the bacterial effector BipD to drive K63-linked ubiquitination of the inner mitochondrial membrane protein IMMT at K211, initiating SQSTM1-dependent mitophagy (PMID:38834545, PMID:39265641). KLHL13 additionally couples with the E2 enzyme UBE2D3 to mediate K63-linked ubiquitination of TAP2 at K245, impairing MHC-I antigen presentation (PMID:41315272). Hemizygous loss-of-function variants in KLHL13 cause an X-linked neurodevelopmental disorder with intellectual disability and macrocephaly; the variants impair mitotic cell-cycle regulation and cause genomic instability that is rescued by AURKB inhibition, establishing dysregulated AURKB control as the disease mechanism (PMID:41159445). KLHL13 protein level is itself stabilized against proteasomal degradation by RHOBTB2 (PMID:41107424) and is transcriptionally controlled downstream of KLF5 in a pathway regulating CEP57L1 stability and centrosome number (PMID:41443421).

1. 2007 High

   Established that KLHL13 is not a free-standing protein but a CUL3 ligase adaptor that directly recognizes Aurora B as substrate, defining its core molecular activity in mitosis.

   Evidence In vitro binding, co-IP, reconstituted and in vivo ubiquitylation, and RNAi mitotic phenotyping

   PMID:17543862

   Open questions at the time

   • Did not resolve how KLHL9 versus KLHL13 contribute distinct substrate-recognition roles within the heterodimer
   • Structural basis of the Kelch domain–AURKB interaction not defined
2. 2007 Medium

   Connected the ligase to checkpoint integrity, showing it is required to sustain spindle assembly checkpoint signaling rather than only to relocalize Aurora B.

   Evidence RNAi knockdown with Cyclin B degradation and mitotic-exit assays under microtubule poisons

   PMID:18075312

   Open questions at the time

   • Whether the SAC defect is a direct consequence of AURKB mislocalization versus an independent function was not separated
   • Single-lab observation
3. 2009 High

   Demonstrated spatial division of labor among CUL3 adaptors, with KLHL9/KLHL13 controlling the chromosomal pool of Aurora B distinctly from KLHL21 at the midzone.

   Evidence Reciprocal adaptor RNAi, live-cell imaging, in vitro ubiquitination, localization studies

   PMID:19995937

   Open questions at the time

   • Did not define what restricts each adaptor to its subcellular pool
   • Relative contributions of KLHL9 and KLHL13 within the shared complex remained unresolved
4. 2017 Medium

   Clarified the neddylation regulation of the complex, showing KLHL9/KLHL13-CUL3 activity is independent of the SCCRO neddylation pathway that controls other CUL3 complexes.

   Evidence SCCRO genetic inactivation with CUL3-adaptor activity assays and adaptor comparisons

   PMID:28620047

   Open questions at the time

   • The actual neddylation route required for KLHL9/KLHL13-CUL3 activation was not identified
   • Negative result confined to one system
5. 2019 High

   Extended KLHL13 substrate scope beyond mitosis by identifying IRS1 as a degradation target, linking the ligase to insulin signaling.

   Evidence BioID, co-IP, siRNA rescue, proteasome inhibition, insulin signaling assays

   PMID:31515271

   Open questions at the time

   • Ubiquitination site on IRS1 and chain linkage not mapped
   • Whether KLHL13 directly recognizes IRS1 versus KLHL9 was not dissected
6. 2021 Medium

   Revealed a developmental/pluripotency role for X-linked Klhl13 in embryonic stem cells distinct from MAPK pathway control, broadening its biology beyond E3 substrate targeting.

   Evidence Chromosome-wide CRISPR knockout screen with secondary validation and expression analysis in mouse ESCs

   PMID:33863351

   Open questions at the time

   • The molecular substrate or mechanism underlying pluripotency-factor regulation was not identified
   • Relationship to its CUL3 ligase activity unclear
7. 2024 High

   Showed the complex can be pathogen-hijacked, defining a K63-linked ubiquitination of IMMT at K211 as a trigger for mitophagy exploited for bacterial survival.

   Evidence Co-IP, ubiquitome MS, IMMT K211 mutagenesis, component knockout, mitophagy and bacterial survival assays

   PMID:38834545 PMID:39265641

   Open questions at the time

   • Whether IMMT is a physiological substrate independent of bacterial BipD was not established
   • How K63 versus K48 linkage choice is determined for this complex unclear
8. 2025 High

   Provided direct human genetic and cross-species causal evidence that KLHL13 loss-of-function causes an X-linked neurodevelopmental disorder via dysregulated AURKB activity.

   Evidence Exome sequencing, HEK293T mitotic/genomic-instability assays, zebrafish knockdown with WT vs variant mRNA rescue, AURKB inhibitor rescue

   PMID:41159445

   Open questions at the time

   • How mitotic genomic instability translates into the macrocephaly/ID phenotype at the neuronal level not resolved
   • Variant-specific effects on non-AURKB substrates not examined
9. 2025 Medium

   Identified an upstream stabilizer of KLHL13, showing RHOBTB2 binds KLHL13 and protects it from proteasomal degradation.

   Evidence Co-IP, western blot, MG132 rescue, overexpression and knockdown

   PMID:41107424

   Open questions at the time

   • Single Co-IP without reciprocal structural mapping of the interaction
   • Whether RHOBTB2 acts as an adaptor or competitor for KLHL13 turnover unclear
10. 2025 High

    Established an E2-partner-dependent immune function, with UBE2D3 directing KLHL13-mediated K63 ubiquitination of TAP2 to suppress antigen presentation in cancer.

    Evidence Co-IP, K63 site-specific mutagenesis at TAP2 K245, antigen presentation assays, genetic/pharmacological inhibition

    PMID:41315272

    Open questions at the time

    • Whether TAP2 targeting requires the full KLHL9/CUL3 complex or KLHL13 alone not resolved
    • Single-lab finding in pancreatic cancer context
11. 2025 Medium

    Placed KLHL13 in a transcriptional axis controlling centrosome number, downstream of KLF5 and regulating CEP57L1 stability.

    Evidence AGE treatment of HCT116, knockdown/overexpression with protein stability readout, mouse metastasis model, patient cohort

    PMID:41443421

    Open questions at the time

    • Whether CEP57L1 is a direct KLHL13/CUL3 substrate not demonstrated
    • Causal contribution of KLHL13 versus CUL3 in CEP57L1 control not separated

• How KLHL13 selects among its diverse substrates (AURKB, IRS1, IMMT, TAP2, CEP57L1) and what determines K48 versus K63 chain output across these contexts remains unresolved.
• No unifying structural model of substrate engagement
• Determinants of chain-linkage choice across substrates unknown
• Relationship between mitotic, metabolic, mitophagy, and immune functions not integrated