Affinage

HYPK

Huntingtin-interacting protein K · UniProt Q9NX55

Length
121 aa
Mass
13.7 kDa
Annotated
2026-06-10
22 papers in source corpus 20 papers cited in narrative 20 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 9/9 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

HYPK is an intrinsically disordered protein that couples regulation of cotranslational N-terminal acetylation to cellular proteostasis (PMID:20154145, PMID:18076027). It is a stable, ribosome-associated subunit of the NatA acetyltransferase complex (Naa10/Naa15), associating with polysomes and required for N-terminal acetylation of NatA substrates (PMID:20154145, PMID:35704578). Structural work defined a bipartite mechanism: HYPK's C-terminal UBA domain binds a metazoan-specific Naa15 region while its N-terminal loop-helix distorts the Naa10 active site to inhibit NatA in vitro, and HYPK binding competitively blocks Naa50 (NatE) recruitment, with HYPK and Naa50 binding NatA/NatE with negative cooperativity (PMID:29754825, PMID:28585574, PMID:32042062). The paradox of in vitro inhibition versus in vivo requirement is resolved by HYPK acting as a ribosome exchange factor that accelerates NatA dissociation from ribosomes, enabling sub-stoichiometric NatA to undergo multiple acetylation turnovers across the nascent proteome (PMID:41380682). Independently of NatA, HYPK is a chaperone that binds Huntingtin via the HTT-N17 domain and engages other aggregation-prone proteins through its C-terminal hydrophobic/NPAA region, suppressing toxic aggregation and self-oligomerizing into annular sequestration complexes (PMID:17947297, PMID:25446099, PMID:25116620, PMID:29458128). It additionally serves as an autophagy receptor for polyneddylated aggregates, bridging NEDD8 (via its UBA domain) and LC3 (via an N-terminal LIR) to promote aggrephagy (PMID:34836490, PMID:27067261). HYPK expression is driven by HSF1 at its promoter under heat shock, and HYPK in turn acts as a negative-feedback repressor of HSF1 transcriptional activity (PMID:24465598, PMID:24361604, PMID:27017930). HYPK also stabilizes Pak1-phosphorylated Arl4A/D and promotes their plasma-membrane recruitment to drive cell migration (PMID:35857868). A de novo HYPK variant that enhances its inhibition of NatA causes a neurodevelopmental syndrome with intellectual disability (PMID:40986405).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 2007 High

    Established HYPK as a direct binding partner of Huntingtin with chaperone-like, anti-aggregation activity, defining its first functional role in proteostasis and neurodegeneration.

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

    PMID:17947297

    Open questions at the time
    • Did not define the HTT region bound or the HYPK domain responsible
    • Did not connect chaperone function to any complex or pathway
  2. 2008 Medium

    Defined HYPK as an intrinsically unstructured protein, explaining its conformational plasticity and capacity for multivalent binding.

    Evidence Gel electrophoresis, SEC, circular dichroism, and limited proteolysis with Ca2+ titration

    PMID:18076027

    Open questions at the time
    • No functional consequence of the Ca2+-induced conformational change demonstrated
    • Disorder not linked to specific binding events
  3. 2010 High

    Placed HYPK on the ribosome as a stable NatA-complex interactor required for cotranslational N-terminal acetylation, unifying its chaperone role with translation.

    Evidence IP-MS, polysome fractionation, siRNA knockdown and in vivo acetylation assay of PCNP

    PMID:20154145

    Open questions at the time
    • Did not resolve whether HYPK promotes or inhibits NatA catalysis
    • No structural basis for NatA association
  4. 2014 Medium

    Mapped the chaperone interaction to the HTT-N17 domain and the conserved C-terminal NPAA domain of HYPK, defining the structural determinants of anti-aggregation activity.

    Evidence Co-IP with deletion mapping, co-localization, viability and caspase assays in HD cell models

    PMID:25116620 PMID:25446099

    Open questions at the time
    • Single-lab domain mapping without structural confirmation
    • Relationship between NPAA chaperone function and NatA binding unresolved
  5. 2014 Medium

    Identified HSF1 as a direct transcriptional driver of HYPK under heat stress, embedding HYPK in the heat shock response.

    Evidence ChIP, reporter assays, RT-PCR and knockdown with viability readouts (two independent labs)

    PMID:24361604 PMID:24465598

    Open questions at the time
    • Did not establish how HYPK protein protects against heat shock mechanistically
    • Did not address feedback onto HSF1
  6. 2016 Medium

    Showed HYPK is a negative-feedback repressor of HSF1, closing an autoregulatory loop and linking HYPK downregulation to Huntington's disease pathology.

    Evidence ChIP, luciferase reporter and knockdown in normal and HD model cells

    PMID:27017930

    Open questions at the time
    • Mechanism of HSF1 repression by HYPK not defined
    • Single-lab study
  7. 2017 High

    Provided the first crystal structures of NatA/HYPK, defining the bipartite binding-plus-inhibition architecture: C-terminal HYPK binds Naa15 while the N-terminal region inhibits acetylation.

    Evidence X-ray crystallography with bi-substrate analogue plus in vitro acetylation assays

    PMID:28585574

    Open questions at the time
    • In vitro inhibition contradicted in vivo requirement for acetylation
    • Did not address Naa50/NatE
  8. 2018 High

    Refined the inhibitory mechanism, showing the HYPK N-terminal loop-helix distorts the Naa10 active site and HYPK blocks Naa50 recruitment to NatA, and expanded the chaperone model to annular sequestration of diverse aggregation-prone proteins.

    Evidence Crystallography with biochemical/enzymatic validation (PMID 29754825); EM and binding assays of HYPK self-oligomerization (PMID 29458128)

    PMID:29458128 PMID:29754825

    Open questions at the time
    • The in vitro vs in vivo paradox of NatA regulation persisted
    • Annular complex structure characterized only by EM in a single lab
  9. 2020 High

    Defined negative cooperativity between HYPK and Naa50 on the NatE complex, with HYPK inducing opposing NAA15 conformational shifts and inhibiting both NAA10 and NAA50 activity.

    Evidence Cryo-EM of NatE and NatE/HYPK with biochemical, enzymatic and in-cell Co-IP validation

    PMID:32042062

    Open questions at the time
    • Physiological balance between competing HYPK and Naa50 binding in cells not quantified
    • Did not resolve net effect on cotranslational acetylation
  10. 2021 High

    Established HYPK as an autophagy receptor for polyneddylated aggregates, bridging NEDD8 and LC3 to drive aggrephagy, extending its role from sequestration to clearance.

    Evidence Co-IP, SPR, domain-specific mutations and autophagy flux/clearance assays

    PMID:34836490

    Open questions at the time
    • In vivo selectivity for neddylated versus ubiquitinated cargo not fully defined
    • Connection to NatA function unaddressed
  11. 2022 Medium

    Demonstrated conservation of the HYPK-NatA function in plants and revealed an unrelated role in Pak1/Arl4A-D signaling, broadening HYPK's functional repertoire.

    Evidence N-terminomics and human-HYPK rescue in Arabidopsis (PMID 35704578); phosphoproteomics, kinase assays, phospho-dependent Co-IP and migration assays (PMID 35857868)

    PMID:35704578 PMID:35857868

    Open questions at the time
    • Arl4A/D pathway studied in one lab
    • Whether NatA association and Arl4 stabilization are mechanistically linked is unknown
  12. 2025 High

    Resolved the central paradox by recasting HYPK as a ribosome exchange factor that accelerates NatA dissociation to enable multi-turnover, proteome-wide acetylation by sub-stoichiometric NatA, and linked HYPK dysfunction to human disease via a gain-of-inhibition variant.

    Evidence In vitro kinetic reconstitution and in-cell biochemistry (PMID 41380682); biochemical assay of variant HYPK with clinical genetics (PMID 40986405)

    PMID:40986405 PMID:41380682

    Open questions at the time
    • Structural basis of the exchange-factor cycle on the ribosome not visualized
    • How the disease variant's enhanced inhibition maps onto exchange-factor kinetics not defined

Open questions

Synthesis pass · forward-looking unresolved questions
  • How HYPK's distinct activities — NatA exchange factor, aggregate chaperone/autophagy receptor, HSF1 repressor, and Arl4 stabilizer — are coordinated or partitioned within the cell remains unresolved.
  • No integrated model linking ribosomal and non-ribosomal pools of HYPK
  • Regulation governing which function dominates under given conditions is unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0044183 protein folding chaperone 4 GO:0098772 molecular function regulator activity 4 GO:0060090 molecular adaptor activity 2 GO:0140110 transcription regulator activity 1
Localization
GO:0005840 ribosome 2 GO:0005634 nucleus 1 GO:0005829 cytosol 1 GO:0005886 plasma membrane 1
Pathway
R-HSA-392499 Metabolism of proteins 4 R-HSA-8953897 Cellular responses to stimuli 3 R-HSA-9612973 Autophagy 2
Partners
ARL4AARL4DHSF1HTTNAA10NAA15NAA50NEDD8
Complex memberships
NatA (Naa10/Naa15)NatE (NAA10/NAA50/NAA15)

Evidence

Reading pass · 20 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, hNaa10p, and hNaa15p associate with polysome fractions, indicating cotranslational function. HYPK knockdown results in increased aggregation of Htt-EGFP with expanded polyQ, and is required for N-terminal acetylation of the NatA substrate PCNP. Immunoprecipitation coupled with mass spectrometry, polysome fractionation, siRNA knockdown, in vivo acetylation assay Molecular and cellular biology High 20154145
2007 HYPK physically interacts with N-terminal Huntingtin in Neuro2A cells, reduces polyQ-mediated aggregate formation, alters aggregate dynamics (FRAP showing ~80% fluorescence recovery), reduces caspase-2, -3, and -8 activations induced by mutant Htt, and exhibits chaperone-like activity in vitro and in vivo. Co-immunoprecipitation, FRAP, FLIP, caspase activity assays, in vitro chaperone assay Human molecular genetics High 17947297
2018 Crystal structures of hNatA and hNatA/HYPK revealed that: (1) hNatA contains a stabilizing inositol hexaphosphate (IP6) molecule and a metazoan-specific Naa15 domain; (2) HYPK harbors intrinsic hNatA-specific inhibitory activity through a bipartite structure—a C-terminal ubiquitin-associated (UBA) domain that binds a metazoan-specific Naa15 region, and an N-terminal loop-helix region that distorts the hNaa10 active site; (3) HYPK binding blocks hNaa50 targeting to hNatA, likely limiting Naa50 ribosome localization in vivo. X-ray crystallography, biochemical binding assays, enzymatic acetylation assays, in vivo co-immunoprecipitation Structure High 29754825
2017 Crystal structures of NatA bound to HypK (with and without a bi-substrate analogue) showed that HypK C-terminal region mediates high-affinity interaction with the C-terminal part of Naa15, while the HypK N-terminal region acts as a negative regulator of NatA acetylation activity, as confirmed by acetylation assays. X-ray crystallography, in vitro acetylation assays, binding affinity measurements Nature communications High 28585574
2020 Cryo-EM structures of human NatE (NAA10/NAA50/NAA15) and NatE/HYPK complexes revealed that NAA50 and HYPK exhibit negative cooperative binding to NAA15, inducing NAA15 conformational shifts in opposing directions. Both NAA50 and HYPK inhibit NAA10 activity through structural alteration of the NAA10 substrate-binding site. HYPK also structurally alters the NatE substrate-binding site to inhibit NAA50 activity. Cryo-EM structure determination, in vitro biochemical binding assays, enzymatic acetylation assays, in-cell co-immunoprecipitation Nature communications High 32042062
2008 HYPK is an intrinsically unstructured protein (IUP) with premolten globule-like conformation, as determined by gel electrophoresis, size exclusion chromatography, circular dichroism (63% random coil), and limited proteolysis. HYPK undergoes conformational changes in response to increasing Ca2+ concentration. Gel electrophoresis, size exclusion chromatography, circular dichroism spectroscopy, limited proteolysis, mass spectrometry Proteins Medium 18076027
2012 HYPK interacts with EEF1A1, HSPA1A, HTT, LMNB2, TP53, and RELA in neuronal cells, identified by pull-down/MS and confirmed by Co-IP and co-localization. HYPK knockdown decreased cell growth and luciferase refolding ability, increased cytotoxicity, and altered cell cycle phase distribution. Pull-down assay coupled with mass spectrometry, co-immunoprecipitation, co-localization, siRNA knockdown with cell viability and refolding assays PloS one Medium 23272104
2014 HYPK interacts specifically with the N-terminal 17 amino acid domain (HTT-N17) of Huntingtin, and this interaction is crucial for HYPK's chaperone activity. Deletion of HTT-N17 leads to formation of smaller, SDS-soluble nuclear aggregates with increased cytotoxicity. Co-immunoprecipitation, deletion mutant analysis, cell cytotoxicity assay Biochemical and biophysical research communications Medium 25446099
2014 The conserved C-terminal nascent polypeptide-associated alpha (NPAA) domain of HYPK is required for its chaperone-like activity. This domain interacts with nascent proteins, co-localizes with Huntingtin, increases cell viability, and decreases caspase activities in an HD cell model. Sequence conservation analysis, co-localization microscopy, cell viability assay, caspase activity assay with C-terminal domain overexpression Journal of biosciences Medium 25116620
2021 HYPK functions as an autophagy receptor for polyneddylated protein aggregates (aggrephagy). HYPK's C-terminal UBA domain binds NEDD8, and its N-terminal tyrosine-type LC3-interacting region (LIR) binds LC3. Both NEDD8 and HYPK positively regulate basal and proteotoxicity-induced autophagy, protecting cells from aggregates of mutant HTT exon 1. Co-immunoprecipitation, surface plasmon resonance, domain deletion/mutation analysis, autophagy flux assays, siRNA knockdown with aggregate clearance readout Autophagy High 34836490
2018 HYPK acts as a global aggregation-regulatory protein by forming unique annular-shaped sequestration complexes with aggregation-prone proteins (HTT97Q exon 1, α-Synuclein-A53T, SOD1-G93A). The C-terminal hydrophobic region of HYPK makes direct contacts with aggregates. HYPK self-oligomerizes in a concentration-dependent, seed nucleation-dependent manner to form annular structures. Co-immunoprecipitation, affinity binding assays, electron microscopy, cell biology assays with overexpression Journal of molecular biology Medium 29458128
2016 HYPK overexpression increases autophagy (LC3-I to LC3-II conversion, BECN1 expression, ATG5-ATG12 conjugation, transcription factor changes), while HYPK knockdown decreases autophagy in striatal cells. HYPK overexpression partially rescues the reduction in LC3-II and BECN1 caused by mutant HTT. Overexpression and siRNA knockdown in striatal cell lines, Western blot for LC3, BECN1, ATG5-ATG12, GFP-LC3 cleavage assay European journal of cell biology Medium 27067261
2014 HSF1 directly binds to the HYPK promoter in a heat-inducible manner (confirmed by chromatin immunoprecipitation) and maintains HYPK expression under heat shock. HSF1 knockdown reduces HYPK expression. Histone H4 acetylation at the HYPK promoter is induced by heat shock. HYPK overexpression protects cells from lethal heat shock, while HYPK knockdown increases susceptibility. Chromatin immunoprecipitation, reporter assay, RT-PCR, Western blot, siRNA knockdown, cell viability assay PloS one Medium 24465598
2013 HSF1 binds to the HYPK promoter in a heat-inducible manner and maintains HYPK expression in heat-shocked cells. Silencing HYPK in heat-shocked cells decreases cell viability. Chromatin immunoprecipitation, RT-PCR, Western blot, siRNA knockdown, cell viability assay Biochimica et biophysica acta Medium 24361604
2016 HYPK acts as a negative regulator of the heat shock response by repressing HSF1 transcriptional activity, including repressing HSF1-dependent transactivation of its own promoter (autoregulatory loop). HYPK is downregulated in HD cell and animal models due to reduced HSF1 occupancy at the HYPK promoter, and mutant huntingtin impairs heat-induced HYPK induction. Chromatin immunoprecipitation, luciferase reporter assay, siRNA knockdown, Western blot, ChIP in HD model cells Experimental cell research Medium 27017930
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). The full-length HYPK (but not HYPK-ΔN) translocates to the nucleus and prevents aggregation of mutant p53 (p53-R248Q) and modulates cell cycle. The NLS is present exclusively in higher eukaryotes. IRES reporter assay, site-directed mutagenesis of start codon, cellular localization microscopy, mutant p53 aggregation assay, cell cycle analysis RNA biology Medium 31397627
2022 Fibronectin stimulation induces Pak1-mediated phosphorylation at S143 of Arl4A and S144 of Arl4D, which promotes HYPK binding to Arl4A/D. HYPK binding stabilizes Arl4A/D by preventing proteasomal degradation and facilitates their recruitment to the plasma membrane to promote cell migration. Proteomic/phosphoproteomic analysis, in vitro kinase assay, co-immunoprecipitation, siRNA knockdown, cell migration assay, confocal microscopy Proceedings of the National Academy of Sciences of the United States of America High 35857868
2022 AtHYPK (Arabidopsis ortholog) physically interacts with the ribosome-anchoring subunit of NatA and promotes Nα-terminal acetylation of NatA substrates in vivo, including facilitating masking of the nonAc-X2/N-degron to prevent proteasomal degradation. Ectopic expression of human HYPK rescues the AtHYPK loss-of-function phenotype. Co-immunoprecipitation, N-terminomics, proteomics, transcriptomics, genetic complementation with human HYPK Science advances Medium 35704578
2025 HYPK acts as a ribosome exchange factor for NatA. Without HYPK, NatA binds ribosomes hyper-tightly, preventing it from accessing additional ribosomes for successive rounds of acetylation. HYPK accelerates NatA dissociation from the ribosome, enabling multiple turnovers and allowing sub-stoichiometric NatA to globally acetylate the nascent proteome. This resolves the paradox of HYPK inhibiting NatA in vitro but enhancing function in vivo. Kinetic measurements (in vitro), in-cell biochemical measurements, ribosome binding assays, NatA acetylation assays with and without HYPK Molecular cell High 41380682
2025 A de novo pathogenic HYPK variant enhances the inhibitory activity of HYPK on NatA-mediated N-terminal protein acetylation, as demonstrated by biochemical analysis, and causes a neurodevelopmental syndrome with intellectual disability and developmental delay. Biochemical NatA acetylation assay with variant HYPK protein, clinical genetic analysis Clinical genetics Medium 40986405

Source papers

Stage 0 corpus · 22 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 120 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 73 17947297
2018 Structure of Human NatA and Its Regulation by the Huntingtin Interacting Protein HYPK. Structure (London, England : 1993) 69 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
2022 HYPK promotes the activity of the Nα-acetyltransferase A complex to determine proteostasis of nonAc-X2/N-degron-containing proteins. Science advances 30 35704578
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
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 12 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
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

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