Affinage

KLHDC10

Kelch domain-containing protein 10 · UniProt Q6PID8

Length
442 aa
Mass
49.1 kDa
Annotated
2026-04-28
93 papers in source corpus 3 papers cited in narrative 3 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

KLHDC10 is a kelch-repeat protein that functions both as an inhibitor of protein phosphatase 5 (PP5) and as a substrate receptor in the CRL2 E3 ubiquitin ligase complex. It binds the phosphatase domain of PP5 and suppresses its activity, thereby sustaining ROS-induced activation of the pro-apoptotic kinase ASK1 and promoting oxidative stress-induced cell death (PMID:23102700). As the substrate-recognition subunit of CRL2-KLHDC10, it directly recognizes C-terminal polyalanine (Ala-tail) degrons on aberrant nascent polypeptides produced during ribosome-associated quality control (RQC), targeting them for ubiquitylation and proteasomal degradation (PMID:37676773).

Mechanistic history

Synthesis pass · year-by-year structured walk · 3 steps
  1. 2012 High

    Establishing KLHDC10 as a regulator of stress-induced apoptosis resolved how ROS-activated ASK1 signaling is sustained: KLHDC10 directly binds and inhibits PP5 phosphatase activity, preventing PP5-mediated dephosphorylation and inactivation of ASK1.

    Evidence Proteomics screen, reciprocal Co-IP, in vitro phosphatase assay, Drosophila genetic screen, and siRNA knockdown in mammalian Neuro2A cells

    PMID:23102700

    Open questions at the time
    • Structural basis of KLHDC10–PP5 interaction not determined
    • Whether KLHDC10 regulates PP5 substrates beyond ASK1 is unknown
    • Physiological relevance in mammalian tissues in vivo not established in this study
  2. 2016 Medium

    Extending KLHDC10 function in vivo, knockout mice revealed that KLHDC10 deficiency selectively enhances necroptosis in inflammatory cells during TNFα-induced SIRS, dampening the cytokine response — demonstrating a role in modulating inflammatory cell death distinct from its ASK1-apoptosis axis.

    Evidence KLHDC10 knockout mouse model with TNFα-induced systemic inflammatory response syndrome and in vitro cell death assays

    PMID:27631783

    Open questions at the time
    • Molecular mechanism linking KLHDC10 to necroptosis pathway components (e.g., RIPK1/RIPK3/MLKL) not identified
    • Single-lab study; independent replication in additional inflammatory models lacking
    • Whether PP5 inhibition mediates the necroptosis phenotype was not tested
  3. 2023 High

    Identification of KLHDC10 as the CRL2 substrate receptor for C-terminal polyalanine degrons established its role in ribosome-associated quality control — a function mechanistically distinct from its PP5 inhibition — and showed that the Ala-tail binding pocket evolved by repurposing a conserved C-degron recognition module.

    Evidence Biochemical binding assays, structure-guided mutagenesis of predicted Ala-tail binding pocket, and evolutionary sequence analysis

    PMID:37676773

    Open questions at the time
    • High-resolution experimental structure of KLHDC10 bound to an Ala-tail substrate not yet available
    • In vivo contribution of KLHDC10-mediated Ala-tail ubiquitylation to RQC pathway flux not quantified
    • Relationship between the two known functions (PP5 inhibition vs. CRL2 substrate receptor) is unresolved

Open questions

Synthesis pass · forward-looking unresolved questions
  • It remains unknown how the dual functions of KLHDC10 — PP5 inhibition in stress signaling and CRL2-mediated ubiquitylation in ribosome quality control — are coordinated or independently regulated in different cellular contexts.
  • No structural data resolving whether PP5-binding and CRL2-adaptor surfaces overlap
  • Tissue-specific regulation of the two functions is uncharacterized
  • Mechanism linking KLHDC10 to necroptosis at the molecular level remains unidentified

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098772 molecular function regulator activity 1 GO:0140096 catalytic activity, acting on a protein 1
Localization
GO:0005829 cytosol 1
Pathway
R-HSA-5357801 Programmed Cell Death 2 GO:0005829 cytosol 1 R-HSA-392499 Metabolism of proteins 1
Partners
Complex memberships
CRL2-KLHDC10

Evidence

Reading pass · 3 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2012 KLHDC10 (mammalian ortholog of Drosophila Slim) interacts with Protein phosphatase 5 (PP5) by binding to the phosphatase domain of PP5 and suppressing its phosphatase activity, thereby enabling sustained ROS-induced activation of ASK1 and promoting oxidative stress-induced cell death. Proteomics screen, Co-IP, in vitro phosphatase activity assay, Drosophila misexpression screen, siRNA knockdown in Neuro2A cells Molecular cell High 23102700
2016 KLHDC10 deficiency selectively enhances necroptosis in inflammatory cells encountering DAMPs, reducing the inflammatory cytokine response in TNFα-induced systemic inflammatory response syndrome (SIRS) in mice, without affecting early systemic necroptosis. KLHDC10 knockout mouse model, TNFα-induced SIRS model, in vitro cell death assays PloS one Medium 27631783
2023 KLHDC10, as part of the CRL2-KLHDC10 E3 ligase complex, directly binds C-terminal polyalanine (Ala-tail) degrons generated during ribosome-associated quality control (RQC) of stalled translation products; the Ala-tail-binding pocket of KLHDC10 was structurally predicted and experimentally validated, and this recognition element evolved by tinkering of a widespread C-degron-recognition module. Biochemical binding assays, in silico structural prediction with experimental validation, mutagenesis of candidate pocket residues, evolutionary sequence analysis Cell reports High 37676773

Source papers

Stage 0 corpus · 93 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2019 PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic acids research 2170 30407594
2011 Spatial light interference microscopy (SLIM). Optics express 356 21263640
2004 Site-directed, Ligase-Independent Mutagenesis (SLIM): a single-tube methodology approaching 100% efficiency in 4 h. Nucleic acids research 288 15585660
2005 SLIM is a nuclear ubiquitin E3 ligase that negatively regulates STAT signaling. Immunity 168 15963787
2019 Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes. Molecular ecology resources 159 30565882
2000 Expression patterns of FHL/SLIM family members suggest important functional roles in skeletal muscle and cardiovascular system. Mechanisms of development 152 10906474
2013 SLiM: simulating evolution with selection and linkage. Genetics 141 23709637
2016 Expanding the PP2A Interactome by Defining a B56-Specific SLiM. Structure (London, England : 1993) 126 27998540
2016 Effectiveness of methotrexate with step-down glucocorticoid remission induction (COBRA Slim) versus other intensive treatment strategies for early rheumatoid arthritis in a treat-to-target approach: 1-year results of CareRA, a randomised pragmatic open-label superiority trial. Annals of the rheumatic diseases 83 27432356
1996 Slim defines a novel family of LIM-proteins expressed in skeletal muscle. Biochemical and biophysical research communications 72 8753811
2020 SLIM: A Short-Linked, Highly Redox-Stable Trityl Label for High-Sensitivity In-Cell EPR Distance Measurements. Angewandte Chemie (International ed. in English) 67 32329172
2012 The Kelch repeat protein KLHDC10 regulates oxidative stress-induced ASK1 activation by suppressing PP5. Molecular cell 67 23102700
2014 Cochlear implantation with the nucleus slim straight electrode in subjects with residual low-frequency hearing. Ear and hearing 58 24556970
2011 BSP-SLIM: a blind low-resolution ligand-protein docking approach using predicted protein structures. Proteins 56 21971880
2019 SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data. BMC bioinformatics 46 30782112
2007 Plasma levels of leptin, omentin, collagenous repeat-containing sequence of 26-kDa protein (CORS-26) and adiponectin before and after oral glucose uptake in slim adults. Cardiovascular diabetology 41 17311679
2021 Ox-SLIM: Synthesis of and Site-Specific Labelling with a Highly Hydrophilic Trityl Spin Label. Chemistry (Weinheim an der Bergstrasse, Germany) 39 33404074
2000 The LIM-domain protein FHL1 (SLIM 1) exhibits functional regulation in skeletal muscle. Molecular cell biology research communications : MCBRC 38 10860860
2023 The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome. Current opinion in structural biology 34 37099901
2016 Investigating the human Calcineurin Interaction Network using the πɸLxVP SLiM. Scientific reports 33 27974827
2007 Uncultivated Tannerella BU045 and BU063 are slim segmented filamentous rods of high prevalence but low abundance in inflammatory disease-associated dental plaques. Microbiology (Reading, England) 33 17975090
2022 Characterization of Phytochemicals, Nutrients, and Antiradical Potential in Slim Amaranth. Antioxidants (Basel, Switzerland) 31 35739986
2011 Associations of lower-body fat mass with favorable profile of lipoproteins and adipokines in healthy, slim women in early adulthood. Journal of atherosclerosis and thrombosis 31 21233589
2007 SLIM: a new method for molecular imaging. Microscopy research and technique 28 17366616
2022 The spindle checkpoint proteins BUB1 and BUBR1: (SLiM)ming down to the basics. Trends in biochemical sciences 25 35184951
2016 A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL. Journal of biomedical semantics 22 27678076
2023 SLiM-binding pockets: an attractive target for broad-spectrum antivirals. Trends in biochemical sciences 20 36623987
2005 SLIM trims STATs: ubiquitin E3 ligases provide insights for specificity in the regulation of cytokine signaling. Science's STKE : signal transduction knowledge environment 19 16204702
2023 Mechanism and evolutionary origins of alanine-tail C-degron recognition by E3 ligases Pirh2 and CRL2-KLHDC10. Cell reports 17 37676773
2022 Ehrlichia SLiM Ligand Mimetic Activates Notch Signaling in Human Monocytes. mBio 15 35357214
2022 Ehrlichia SLiM ligand mimetic activates Hedgehog signaling to engage a BCL-2 anti-apoptotic cellular program. PLoS pathogens 14 35576232
2018 FRET-SLiM on native autofluorescence: a fast and reliable method to study interactions between fluorescent probes and lignin in plant cell wall. Plant methods 14 30154910
2014 [Histopathological particle algorithm. Particle identification in the synovia and the SLIM]. Zeitschrift fur Rheumatologie 14 24821089
2013 Optimized slim-line logging NMR tool to measure soil moisture in situ. Journal of magnetic resonance (San Diego, Calif. : 1997) 14 23757362
2008 Fighting fat with muscle: bulking up to slim down. Cell metabolism 14 18249167
2021 Structural determinants driving the binding process between PDZ domain of wild type human PALS1 protein and SLiM sequences of SARS-CoV E proteins. Computational and structural biotechnology journal 13 33758649
2018 SLIM microscopy allows for visualization of DNA-containing liposomes designed for sperm-mediated gene transfer in cattle. Molecular biology reports 12 30539382
2003 The SLIM spectrometer. Analytical chemistry 11 12530815
2022 Evolution of SLiM-mediated hijack functions in intrinsically disordered viral proteins. Essays in biochemistry 10 36468648
2019 Principles of Ion Selection, Alignment, and Focusing in Tandem Ion Mobility Implemented Using Structures for Lossless Ion Manipulations (SLIM). Journal of the American Society for Mass Spectrometry 10 30963456
2018 SLiM-Enrich: computational assessment of protein-protein interaction data as a source of domain-motif interactions. PeerJ 10 30402352
2010 SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank. Bioinformatics (Oxford, England) 10 20167627
2023 Ehrlichia effector SLiM-icry: Artifice of cellular subversion. Frontiers in cellular and infection microbiology 8 36960039
2023 Ehrlichia Wnt SLiM ligand mimic deactivates the Hippo pathway to engage the anti-apoptotic Yap-GLUT1-BCL-xL axis. Infection and immunity 8 37530530
2017 A Simple Light Isotope Metabolic Labeling (SLIM-labeling) Strategy: A Powerful Tool to Address the Dynamics of Proteome Variations In Vivo. Molecular & cellular proteomics : MCP 8 28821603
2016 In-Phase Assembly of Slim DNA Lattices with Small Circular DNA Motifs via Short Connections of 11 and 16 Base Pairs. Chembiochem : a European journal of chemical biology 8 27187004
2025 SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes. bioRxiv : the preprint server for biology 7 40832315
2020 Not So Slim Anymore-Evidence for the Role of SUMO in the Regulation of Lipid Metabolism. Biomolecules 7 32781719
2016 KLHDC10 Deficiency Protects Mice against TNFα-Induced Systemic Inflammation. PloS one 7 27631783
2013 Predictability of gene ontology slim-terms from primary structure information in Embryophyta plant proteins. BMC bioinformatics 7 23441934
2007 Role of mitochondria in cell death induced by Photofrin-PDT and ursodeoxycholic acid by means of SLIM. Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology 7 18046490
2023 HIV enteropathy and 'Slim disease': Historical and current perspectives. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases 6 38052315
2021 slim shady is a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201. Plant direct 6 34136747
2018 Slim Body Weight Is Highly Associated With Enhanced Lipoprotein Functionality, Higher HDL-C, and Large HDL Particle Size in Young Women. Frontiers in endocrinology 6 30072955
2010 Classifying genes to the correct Gene Ontology Slim term in Saccharomyces cerevisiae using neighbouring genes with classification learning. BMC genomics 6 20509921
2025 The "DDVF" motif used by viral and bacterial proteins to hijack RSK kinases mimics a short linear motif (SLiM) found in proteins related to the RAS-ERK MAP kinase pathway. PLoS pathogens 5 40153681
2025 AlphaFold2 SLiM screen for LC3-LIR interactions in autophagy. Autophagy 5 40320752
2024 The impact of biomarkers of malignancy (IMWG SLiM criteria) in myeloma in a real-world population: Clinical characteristics, therapy and outcomes from the Australian and New Zealand Myeloma and Related Diseases Registry (ANZ MRDR). British journal of haematology 5 38965706
2023 GOgetter: A pipeline for summarizing and visualizing GO slim annotations for plant genetic data. Applications in plant sciences 5 37601315
2022 Slim larks and overweight owls? A two years dietary intervention in shift workers. Industrial health 5 35095034
2011 D-SLIMMER: domain-SLiM interaction motifs miner for sequence based protein-protein interaction data. Journal of proteome research 5 22004555
2023 Switching to lemborexant for the management of insomnia in mental disorders: the SLIM study. Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine 4 37243798
2008 [Latent autoimmune diabetes of adult or slim type 2 diabetes mellitus?]. Arquivos brasileiros de endocrinologia e metabologia 4 18438542
2024 Autologous stem cell transplantation for multiple myeloma patients whose myeloma-defining event was SLiM. British journal of haematology 3 39613336
2023 FAM122A ensures cell cycle interphase progression and checkpoint control as a SLiM-dependent substrate-competitive inhibitor to the B55⍺/PP2A phosphatase. bioRxiv : the preprint server for biology 3 36945596
2023 Retrospective comparative study of new slim-delivery and conventional large-cell stents for stent-in-stent methods for hilar malignant biliary obstruction. Digestive endoscopy : official journal of the Japan Gastroenterological Endoscopy Society 3 37253160
2006 Ultra-slim laminated capillary array for high-speed DNA separation. Electrophoresis 3 16688699
2002 Improved rig for dynamically calibrating skinfold calipers: comparison between Harpenden and Slim Guide instruments. American journal of human biology : the official journal of the Human Biology Council 3 12400032
2025 Enhancing Sensitivity in Low-Load Proteomics Orbitrap Workflows via SLIM Integration. Analytical chemistry 2 40497334
2024 Biophysical and structural analyses of the interaction between the SHANK1 PDZ domain and an internal SLiM. The Biochemical journal 2 38899489
2024 Light-chain amyloidosis with concomitant symptomatic myeloma (CRAB-SLiM features): clinical characteristics, cytogenetic abnormalities, and outcomes. BMC cancer 2 39587494
2022 Efficacy of a novel large-cell Niti-S stent with a slim delivery system for hilar biliary obstruction: a preliminary study. Annals of medicine 2 35412414
2009 [Slim despite a genetic predisposition for obesity--influence of environmental factors as chance? A case report]. Deutsche medizinische Wochenschrift (1946) 2 19421926
2007 Does FASing out new fat in the hypothalamus make you slim? Cell metabolism 2 17908552
2026 Structural Insights into WY Domain SLiM-Containing Conserved RxLR Effectors: A Case Study of Five Important Phytophthora Species. Molecular plant-microbe interactions : MPMI 1 41085491
2025 SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution. bioRxiv : the preprint server for biology 1 40949978
2025 PPI-ID: Streamlining protein-protein interaction prediction through domain and SLiM mapping. PLoS computational biology 1 41100562
2024 Evaluation of a Reference-Free Collision Cross Section Calibration Strategy for Proteomics Using SLIM-Based High-Resolution Ion Mobility Spectrometry-Mass Spectrometry. Journal of the American Society for Mass Spectrometry 1 38864778
2024 SLIM-assisted automatic cartography of cell death types and rates resulting from localized photodynamic treatment. Journal of the Optical Society of America. A, Optics, image science, and vision 1 39889066
2023 A SLiM-dependent conformational change in baculovirus IE1 controls its focus formation ability. The Journal of general virology 1 37877992
2009 Solid-liquid interface method (SLIM): a new crystallization method for proteins. Biochemical and biophysical research communications 1 19545537
2026 SLiM 5: Eco-evolutionary Simulations Across Multiple Chromosomes and Full Genomes. Molecular biology and evolution 0 41292177
2026 Real-world outcomes of SLiM-only multiple myeloma: Korean Multicenter Retrospective analysis (KMM2401 study). Annals of hematology 0 41649556
2026 Modified cell-to-cell method for slim tube test simulation considering the porous media effect. Scientific reports 0 41680269
2026 Pilot study of epigenetic aging and treatment response to semaglutide in the SLIM LIVER study. npj aging 0 42014432
2025 SLIMPHONY: A SLIM-Based Instrument That Orchestrates Complex Ion Mobility-Mass Spectrometry Experiments. Journal of the American Society for Mass Spectrometry 0 41001983
2025 A simple workflow to identify novel small linear motif (SLiM)-mediated interactions with AlphaFold. Briefings in bioinformatics 0 41016010
2025 Epigenetic Aging and Treatment Response to Semaglutide in the SLIM LIVER Study. Research square 0 41256006
2024 Small-group originating model: Optimized individual-level GWAS simulation featured by SLiM and using open-access data. Computational biology and chemistry 0 39033733
2024 Molecular investigate of slim and adhesion genes of Staphylococcus saprophyticus isolated from pregnant women with asymptomatic bacteriuria in Thi-Qar governorates. Wiadomosci lekarskie (Warsaw, Poland : 1960) 0 39548999
2023 Extending the Range of SLIM-Labeling Applications: From Human Cell Lines in Culture to Caenorhabditis elegans Whole-Organism Labeling. Journal of proteome research 0 36748112
2023 The role of aromatase inhibitors in slim women with breast cancer-related lymphoedema: a reflective case series. British journal of community nursing 0 37757816
2023 A phenotypic screen with Trypanosoma brucei for discovering small molecules that target the SLiM-binding pocket of proliferating cell nuclear antigen orthologs. Chemical biology & drug design 0 37767622