Affinage

HYPK

Huntingtin-interacting protein K · UniProt Q9NX55

Length
121 aa
Mass
13.7 kDa
Annotated
2026-04-28
23 papers in source corpus 18 papers cited in narrative 18 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

HYPK is an intrinsically disordered protein that serves as a ribosome exchange factor for the NatA N-terminal acetyltransferase complex, accelerating NatA dissociation from ribosomes after each acetylation event to enable sub-stoichiometric NatA to globally acetylate the nascent proteome (PMID:41380682). Its bipartite architecture—a C-terminal UBA domain anchoring it to Naa15 and an N-terminal loop-helix region that distorts the Naa10 active site—explains its in vitro inhibitory activity while functioning in vivo as a processivity factor for cotranslational acetylation (PMID:28585574, PMID:29754825). Independent of NatA, HYPK functions as a chaperone that senses and sequesters aggregation-prone proteins including polyglutamine-expanded Huntingtin and mutant p53, and acts as an autophagy receptor that bridges polyneddylated aggregates to LC3 for autophagic clearance (PMID:17947297, PMID:29458128, PMID:34836490). A de novo pathogenic HYPK variant that enhances NatA inhibition causes a neurodevelopmental syndrome with intellectual disability (PMID:40986405).

Mechanistic history

Synthesis pass · year-by-year structured walk · 14 steps
  1. 2007 High

    The first functional role for HYPK was established as a chaperone-like protein that physically interacts with Huntingtin and suppresses polyglutamine aggregate-induced apoptosis, answering whether HYPK had any cellular function beyond its identification as a Huntingtin-interacting protein.

    Evidence Co-IP, FRAP/FLIP live-cell imaging, caspase activity assays, and in vitro chaperone assay in Neuro2A cells

    PMID:17947297

    Open questions at the time
    • Mechanism of chaperone activity unknown
    • Whether HYPK has functions beyond Huntingtin interaction not addressed
    • Structural basis of Htt interaction undefined
  2. 2008 Medium

    Biophysical characterization revealed HYPK is an intrinsically disordered protein with a premolten globule-like conformation that undergoes Ca²⁺-induced compaction, establishing the structural framework for understanding how HYPK engages multiple binding partners.

    Evidence CD spectroscopy, size exclusion chromatography, limited proteolysis, SDS-PAGE anomaly

    PMID:18076027

    Open questions at the time
    • Physiological relevance of Ca²⁺-induced conformational change unknown
    • No atomic-resolution structural information
  3. 2010 High

    Discovery that HYPK is a stable subunit of the NatA N-terminal acetyltransferase complex on polysomes established a dual identity for HYPK—linking its chaperone function with cotranslational N-terminal acetylation—and showed that HYPK is required for in vivo NatA substrate acetylation.

    Evidence Co-IP/MS, polysome fractionation, siRNA knockdown with acetylation and Htt aggregation readouts

    PMID:20154145

    Open questions at the time
    • Structural basis of NatA-HYPK interaction unknown
    • Paradox of why HYPK is needed for NatA activity in vivo unresolved
  4. 2012 Medium

    Interactome mapping expanded HYPK's network to include EEF1A1, HSPA1A, TP53, RELA, and LMNB2, and knockdown phenotypes (reduced growth, impaired protein refolding, altered cell cycle) indicated broader proteostasis and cell cycle roles.

    Evidence Pulldown/MS, Co-IP, co-localization, knockdown with luciferase refolding and cell cycle analysis in neuronal cells

    PMID:23272104

    Open questions at the time
    • Direct vs. indirect interactions not distinguished for most partners
    • Mechanism of cell cycle regulation unclear
  5. 2014 Medium

    Three studies refined HYPK's chaperone mechanism and transcriptional regulation: the C-terminal NPAA domain mediates nascent protein binding and chaperone activity, the Htt-N17 domain is the specific HYPK recognition element, and HSF1 directly activates HYPK transcription via promoter binding.

    Evidence Domain deletion/overexpression, co-localization, ChIP/reporter assays, cell viability, deletion mutagenesis of Htt-N17

    PMID:24465598 PMID:25116620 PMID:25446099

    Open questions at the time
    • Whether NPAA domain corresponds to the UBA domain identified crystallographically not clarified
    • Functional significance of HSF1-HYPK axis beyond heat shock not explored
  6. 2016 Medium

    HYPK was shown to negatively regulate HSF1 transcriptional activity—including repression of its own promoter—creating an autoregulatory feedback loop, and was independently linked to positive regulation of autophagy through LC3-II conversion and BECN1 expression.

    Evidence ChIP, reporter assays, overexpression/knockdown with HSP expression and autophagy marker readouts in striatal cell lines

    PMID:27017930 PMID:27067261

    Open questions at the time
    • Direct mechanism by which HYPK represses HSF1 unknown
    • Whether autophagy regulation is direct or indirect through NatA/chaperone functions unresolved
  7. 2017 High

    Crystal structures of NatA-HYPK complexes revealed the bipartite binding mechanism: the HYPK C-terminal region mediates high-affinity Naa15 binding while the N-terminal region inhibits Naa10 catalytic activity, resolving how HYPK both stably associates with and inhibits NatA.

    Evidence X-ray crystallography with and without bi-substrate analogue, acetylation and binding assays

    PMID:28585574

    Open questions at the time
    • Why HYPK inhibits NatA in vitro but promotes acetylation in vivo remained paradoxical
    • Ribosome-bound structure unavailable
  8. 2018 High

    Higher-resolution structures identified the HYPK UBA domain and its metazoan-specific Naa15 binding site, and showed HYPK binding blocks Naa50 targeting to NatA; separately, HYPK was characterized as a global aggregation sensor forming annular sequestration complexes with misfolded proteins via its C-terminal hydrophobic region.

    Evidence X-ray crystallography with active-site mutagenesis; Co-IP/MS interactome, electron microscopy of aggregation complexes, binding affinity measurements

    PMID:29458128 PMID:29754825

    Open questions at the time
    • In vivo significance of HYPK-Naa50 competition unclear
    • Whether annular complexes form in vivo not established
  9. 2019 Medium

    Discovery of IRES-dependent translation producing a truncated HYPK isoform (HYPK-ΔN) lacking the nuclear localization signal revealed that nuclear HYPK prevents mutant p53 aggregation, establishing isoform-specific functional compartmentalization.

    Evidence IRES reporter assay, nuclear localization experiments, mutant p53 aggregation assay, cell cycle analysis

    PMID:31397627

    Open questions at the time
    • Endogenous ratio of full-length to ΔN isoform not quantified
    • Whether nuclear HYPK chaperone activity extends beyond p53 unknown
  10. 2020 High

    Cryo-EM structures of NatE/HYPK complexes revealed negative cooperative binding between HYPK and Naa50 on Naa15, with both HYPK and Naa50 independently inhibiting Naa10 through substrate-binding site alteration, establishing the structural logic of the NatA/NatE/HYPK regulatory network.

    Evidence Cryo-EM, biochemical binding assays, enzymatic activity assays, in-cell binding competition

    PMID:32042062

    Open questions at the time
    • How cells regulate HYPK vs. Naa50 occupancy on NatA in vivo not determined
    • Ribosome-associated complex structure still missing
  11. 2021 High

    HYPK was identified as an autophagy receptor that bridges polyneddylated protein aggregates to autophagosomes via its UBA domain (binding NEDD8) and N-terminal LIR motif (binding LC3), providing a direct mechanistic link between its chaperone and autophagy functions.

    Evidence Co-IP, domain deletion/mutagenesis, SPR, autophagy flux assays, knockdown with aggregation readout

    PMID:34836490

    Open questions at the time
    • Selectivity for polyneddylated vs. polyubiquitinated substrates not fully delineated
    • Whether HYPK receptor function operates during cotranslational quality control unknown
  12. 2022 High

    HYPK was found to stabilize PAK1-phosphorylated Arl4A/D at the plasma membrane, preventing their proteasomal degradation and promoting fibronectin-stimulated cell migration, revealing a NatA-independent chaperoning function at the plasma membrane.

    Evidence Phosphoproteomics, kinase identification, Co-IP, plasma membrane localization, cell migration, proteasome inhibition in fibronectin-stimulated cells

    PMID:35857868

    Open questions at the time
    • Whether HYPK chaperone activity for Arl4A/D requires its UBA or NPAA domain not determined
    • In vivo relevance for tissue migration/invasion not tested
  13. 2025 High

    The long-standing paradox of HYPK inhibiting NatA in vitro but being required for acetylation in vivo was resolved: HYPK functions as a ribosome exchange factor that accelerates NatA dissociation from ribosomes, enabling sub-stoichiometric NatA to perform multiple catalytic turnovers across the nascent proteome.

    Evidence Kinetic measurements, in-cell measurements, ribosome binding assays

    PMID:41380682

    Open questions at the time
    • Structure of ribosome-NatA-HYPK ternary complex not yet solved
    • Whether HYPK exchange factor activity is regulated by post-translational modifications unknown
  14. 2025 Medium

    A de novo HYPK variant was shown to enhance NatA inhibition biochemically and cause a neurodevelopmental syndrome, establishing that HYPK gain-of-inhibitory-function is pathogenic and validating the ribosome exchange factor model in a disease context.

    Evidence Biochemical NatA acetylation activity assay with patient-derived HYPK variant, clinical genetics

    PMID:40986405

    Open questions at the time
    • Single case report; additional patients needed to confirm genotype-phenotype relationship
    • Whether the variant also affects HYPK's chaperone or autophagy receptor functions not tested

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key open questions include: the structure of the ribosome-NatA-HYPK ternary complex; how HYPK's NatA exchange factor, chaperone, autophagy receptor, and Arl4 stabilization functions are coordinated or compartmentalized in vivo; and whether HYPK dysfunction contributes to neurodegeneration beyond Huntington's disease models.
  • No ribosome-bound NatA-HYPK structure available
  • Integration of NatA-dependent and NatA-independent HYPK functions not addressed
  • In vivo animal models with HYPK loss-of-function phenotyping largely absent from primary literature

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098772 molecular function regulator activity 4 GO:0044183 protein folding chaperone 3 GO:0060090 molecular adaptor activity 2 GO:0038024 cargo receptor activity 1
Localization
GO:0005829 cytosol 2 GO:0005840 ribosome 2 GO:0005634 nucleus 1 GO:0005886 plasma membrane 1
Pathway
R-HSA-392499 Metabolism of proteins 4 R-HSA-8953897 Cellular responses to stimuli 2 R-HSA-9612973 Autophagy 2
Partners
ARL4AARL4DHTTLC3NAA10NAA15NAA50NEDD8
Complex memberships
NatA (Naa10/Naa15/HYPK)NatE (Naa10/Naa15/Naa50/HYPK)

Evidence

Reading pass · 18 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2010 HYPK is a stable interactor of the NatA complex (hNaa10p/hNaa15p), identified by immunoprecipitation coupled with mass spectrometry. HYPK associates with polysome fractions alongside NatA subunits, indicating a cotranslational function. Knockdown of HYPK or hNAA10 increased aggregation of polyglutamine-expanded Htt-EGFP, and HYPK is required for N-terminal acetylation of the NatA substrate PCNP. Co-IP/MS, polysome fractionation, siRNA knockdown, Htt-EGFP aggregation assay, in vivo acetylation assay Molecular and cellular biology High 20154145
2007 HYPK physically interacts with N-terminal Huntingtin in Neuro2A cells and modulates polyglutamine aggregate formation and kinetics. HYPK overexpression reduces caspase-2, -3, and -8 activation induced by mutant Htt but not by gamma irradiation. HYPK exhibits chaperone-like activity in vitro and in vivo. Co-IP, FRAP, FLIP, caspase activity assays, in vitro chaperone assay Human molecular genetics High 17947297
2018 Crystal structures of human NatA and NatA/HYPK complexes reveal that HYPK has a bipartite inhibitory mechanism: its ubiquitin-associated (UBA) domain binds a metazoan-specific region of Naa15, while its N-terminal loop-helix region distorts the Naa10 active site to inhibit catalytic activity. HYPK binding blocks Naa50 targeting to NatA, likely limiting Naa50 ribosome localization. NatA also contains a stabilizing inositol hexaphosphate (IP6) molecule. X-ray crystallography, biochemical/enzymatic assays, active-site mutagenesis Structure High 29754825
2017 Crystal structures of NatA bound to HypK (with and without bi-substrate analogue) show that the HypK C-terminal region mediates high-affinity binding to the C-terminal part of Naa15, while the HypK N-terminal region acts as a negative regulator of NatA acetylation activity, demonstrated by acetylation assays. X-ray crystallography, acetylation assays, binding assays Nature communications High 28585574
2020 Cryo-EM structures of human NatE (NAA10/NAA50/NAA15) and NatE/HYPK complexes reveal that HYPK and NAA50 exhibit negative cooperative binding to NAA15, inducing opposing conformational shifts. Both HYPK and NAA50 inhibit NAA10 activity through structural alteration of its substrate-binding site. HYPK inhibits NAA50 activity by structurally altering the NatE substrate-binding site. NAA15 tethering increases NAA50 activity. Cryo-EM structure determination, biochemical binding assays, enzymatic activity assays, in-cell binding competition assays Nature communications High 32042062
2008 HYPK is an intrinsically unstructured protein (premolten globule-like conformation) as determined by gel electrophoresis anomaly, size exclusion chromatography, circular dichroism (63% random coil), and limited proteolysis. HYPK undergoes conformational change and reduction in hydrodynamic radius in response to increasing Ca2+ concentration. SDS-PAGE, size exclusion chromatography, circular dichroism, limited proteolysis, mass spectrometry Proteins Medium 18076027
2014 HYPK interacts specifically with the first 17 amino acids (N17 domain) of Huntingtin. Deletion of HTT-N17 abolishes this interaction and leads to formation of tinier, SDS-soluble nuclear aggregates with increased cytotoxicity, indicating that HYPK's chaperone activity requires interaction with HTT-N17. Co-IP, deletion mutagenesis, cytotoxicity assays, aggregate characterization Biochemical and biophysical research communications Medium 25446099
2014 The conserved C-terminal nascent polypeptide-associated alpha (NPAA) domain of HYPK mediates nascent protein binding, co-localizes with Huntingtin, increases cell viability, and is required for the chaperone-like activity of HYPK in vivo. Sequence analysis, overexpression of domain fragments, co-localization, cell viability assay, caspase activity assay Journal of biosciences Medium 25116620
2012 HYPK interacts with EEF1A1, HSPA1A, HTT, LMNB2, TP53, and RELA in neuronal cells, identified by pulldown/MS followed by co-localization and Co-IP. Knockdown of HYPK decreases cell growth and luciferase refolding ability, increases cytotoxicity, and alters cell cycle phase distribution. Pulldown/MS, Co-IP, co-localization, knockdown, luciferase refolding assay, cell cycle analysis PloS one Medium 23272104
2018 HYPK functions as a global aggregation-regulatory protein that senses aggregation-prone proteins (HTT97Q exon1, α-Synuclein-A53T, SOD1-G93A) via its C-terminal hydrophobic region, forming annular-shaped sequestration complexes. HYPK itself undergoes concentration-dependent self-oligomerization via seed nucleation through two hydrophobic C-terminal segments, forming annular and amorphous aggregates. HYPK preferentially binds aggregation-prone proteins with higher affinity than native proteins. Co-IP/MS interactome screen, in vitro aggregation assays, electron microscopy, binding affinity measurements, cell biology assays Journal of molecular biology Medium 29458128
2021 HYPK functions as an autophagy receptor for polyneddylated protein aggregates. HYPK's C-terminal UBA domain binds NEDD8 and its N-terminal tyrosine-type LC3-interacting region (LIR) binds LC3, scaffolding the delivery of polyneddylated aggregates to autophagosomes. HYPK and NEDD8 are positive modulators of basal and proteotoxicity-induced autophagy, enabling clearance of mutant HTT exon 1 aggregates. Co-IP, domain deletion/mutagenesis, surface plasmon resonance, autophagy flux assays, KD with aggregation phenotype readout Autophagy High 34836490
2019 HYPK mRNA undergoes IRES-dependent translation from an internal start codon to generate a truncated isoform (HSPC136/HYPK-ΔN) lacking the N-terminal tri-arginine nuclear localization signal (NLS). Full-length HYPK translocates to the nucleus and prevents aggregation of mutant p53 (R248Q), whereas HYPK-ΔN lacks this activity. The NLS is present only in higher eukaryotes and allows HYPK to modulate cell cycle from the nucleus. IRES reporter assay, nuclear localization experiments, mutant p53 aggregation assay, cell cycle analysis RNA biology Medium 31397627
2022 Fibronectin stimulation induces PAK1-mediated phosphorylation of Arl4A at S143 and Arl4D at S144, promoting HYPK binding to Arl4A/D. HYPK acts as a chaperone to stabilize Arl4A/D at the plasma membrane, preventing their proteasomal degradation and promoting cell migration. Proteomic phosphorylation analysis, kinase identification, Co-IP, plasma membrane localization assays, cell migration assays, proteasome inhibition experiments Proceedings of the National Academy of Sciences of the United States of America High 35857868
2014 HSF1 regulates HYPK expression by binding to the HYPK promoter in a heat-inducible manner, validated by chromatin immunoprecipitation and reporter assays. HSF1 knockdown reduces HYPK mRNA levels; HYPK knockdown decreases cell viability under heat shock. ChIP, reporter assay, RT-PCR, Western blot, siRNA knockdown, cell viability assay PloS one Medium 24465598
2016 HYPK acts as a negative regulator of heat shock response by repressing HSF1 transcriptional activity, including repression of its own promoter (autoregulatory loop). In HD cell models, HYPK is downregulated due to reduced HSF1 occupancy at the HYPK promoter, and mutant huntingtin impairs heat-inducible HYPK upregulation. ChIP, reporter assay, overexpression/knockdown, HSP expression assays Experimental cell research Medium 27017930
2016 Overexpression of HYPK increases cellular autophagy (LC3-I to LC3-II conversion, BECN1 expression, ATG5-ATG12 conjugate formation), while knockdown decreases autophagy. HYPK overexpression restores LC3-II and BECN1 levels reduced by mutant HTT. Western blot (LC3, BECN1, ATG5-ATG12), GFP-LC3 cleavage assay, siRNA knockdown, overexpression in striatal cell lines European journal of cell biology Medium 27067261
2025 HYPK acts as a ribosome exchange factor for NatA: without HYPK, NatA binds ribosomes too tightly (hyper-tight binding), preventing it from accessing additional ribosomes after each acetylation event. HYPK accelerates NatA dissociation from the ribosome, enabling multiple catalytic turnovers and allowing sub-stoichiometric NatA to globally acetylate the nascent proteome. This resolves the paradox of HYPK inhibiting NatA in vitro while enhancing its function in vivo. Kinetic measurements, in-cell measurements, ribosome binding assays Molecular cell High 41380682
2025 A de novo pathogenic HYPK variant enhances HYPK's inhibitory activity on NatA-mediated N-terminal protein acetylation, demonstrating that gain-of-HYPK-inhibitory-function causes a neurodevelopmental syndrome with intellectual disability, developmental delay, and dysmorphic features. Biochemical analysis of NatA acetylation activity with pathogenic HYPK variant, clinical genetic characterization Clinical genetics Medium 40986405

Source papers

Stage 0 corpus · 23 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2010 The chaperone-like protein HYPK acts together with NatA in cotranslational N-terminal acetylation and prevention of Huntingtin aggregation. Molecular and cellular biology 119 20154145
2007 HYPK, a Huntingtin interacting protein, reduces aggregates and apoptosis induced by N-terminal Huntingtin with 40 glutamines in Neuro2a cells and exhibits chaperone-like activity. Human molecular genetics 71 17947297
2018 Structure of Human NatA and Its Regulation by the Huntingtin Interacting Protein HYPK. Structure (London, England : 1993) 67 29754825
2017 Structural basis of HypK regulating N-terminal acetylation by the NatA complex. Nature communications 60 28585574
2020 Molecular basis for N-terminal acetylation by human NatE and its modulation by HYPK. Nature communications 42 32042062
2012 Identification of HYPK-interacting proteins reveals involvement of HYPK in regulating cell growth, cell cycle, unfolded protein response and cell death. PloS one 30 23272104
2022 HYPK promotes the activity of the Nα-acetyltransferase A complex to determine proteostasis of nonAc-X2/N-degron-containing proteins. Science advances 28 35704578
2008 Huntingtin interacting protein HYPK is intrinsically unstructured. Proteins 25 18076027
2014 Chaperone protein HYPK interacts with the first 17 amino acid region of Huntingtin and modulates mutant HTT-mediated aggregation and cytotoxicity. Biochemical and biophysical research communications 24 25446099
2021 HYPK coordinates degradation of polyneddylated proteins by autophagy. Autophagy 21 34836490
2018 Aggregation-prone Regions in HYPK Help It to Form Sequestration Complex for Toxic Protein Aggregates. Journal of molecular biology 19 29458128
2014 Conserved C-terminal nascent peptide binding domain of HYPK facilitates its chaperone-like activity. Journal of biosciences 16 25116620
2014 Transcription regulation of HYPK by Heat Shock Factor 1. PloS one 15 24465598
2013 Heat shock transcription factor HSF1 regulates the expression of the Huntingtin-interacting protein HYPK. Biochimica et biophysica acta 14 24361604
2019 An IRES-dependent translation of HYPK mRNA generates a truncated isoform of the protein that lacks the nuclear localization and functional ability. RNA biology 13 31397627
2016 Huntingtin interacting protein HYPK is a negative regulator of heat shock response and is downregulated in models of Huntington's Disease. Experimental cell research 13 27017930
2022 Phosphorylation of Arl4A/D promotes their binding by the HYPK chaperone for their stable recruitment to the plasma membrane. Proceedings of the National Academy of Sciences of the United States of America 11 35857868
2018 Metastable states of HYPK-UBA domain's seeds drive the dynamics of its own aggregation. Biochimica et biophysica acta. General subjects 11 30251673
2024 HYPK controls stability and catalytic activity of the N-terminal acetyltransferase A in Arabidopsis thaliana. Cell reports 7 38363676
2016 Chaperone-like protein HYPK and its interacting partners augment autophagy. European journal of cell biology 6 27067261
2024 HYPK: A marginally disordered protein sensitive to charge decoration. Proceedings of the National Academy of Sciences of the United States of America 5 38657047
2025 HYPK-Related Neurodevelopmental Syndrome: Case Report of Intellectual Disability, Developmental Delay, and Dysmorphic Features. Clinical genetics 2 40986405
2025 HYPK promotes N-terminal protein acetylation through rapid ribosome exchange of NatA. Molecular cell 0 41380682