YDJ1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005829 cytosol	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for cytosol localization is well supported. YDJ1 was shown by immunofluorescence to localize to the cytoplasm and perinuclear region (PMID:1869583), and confirmed by large-scale HDA studies (PMID:26928762) and IDA (PMID:8144572). Reason: Cytosol is a well-established localization for YDJ1. Multiple independent methods confirm cytosolic localization. IBA is consistent with IDA evidence from PMID:1869583 and PMID:8144572. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001531327 · PANTHER:PTN001531327 SUPPORTS TRANSFER The current PTHR43888 PAINT record places cytosol at this broad eukaryotic J-protein node using fungal and metazoan descendants. Direct YDJ1 localization evidence independently supports the annotation. Supporting Evidence: file:yeast/YDJ1/YDJ1-deep-research-falcon.md Ydj1 is predominantly cytosolic, but is partially membrane-associated through its C-terminal prenylation (farnesylation)
GO:0001671 ATPase activator activity	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for ATPase activator activity is strongly supported. YDJ1 stimulates the ATPase activity of Hsp70 Ssa1 (PMID:1400408, PMID:9774392), which is the core molecular function of J-domain co-chaperones. Reason: ATPase activator activity is the defining molecular function of the J-domain. Experimentally demonstrated by IDA (PMID:1400408, PMID:15342786) and conserved across the DnaJ family. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN002376157 · PANTHER:PTN002376157 SUPPORTS TRANSFER The PTHR43888 PAINT record places ATPase activator activity at this broad J-protein node; YDJ1 is one of its experimentally grounded descendants, consistent with direct Ssa1 ATPase assays. Supporting Evidence: PMID:1400408 We report that a purified cytoplasmic Hsp70 homolog from Saccharomyces cerevisiae, Hsp70SSA1, exhibits a weak ATPase activity, which is stimulated by a purified eukaryotic dnaJp homolog (YDJ1p). PMID:9774392 This functional difference was explored and could not be accounted for by differences in the ability of Sis1 and Ydj1 to regulate Ssa1 ATPase activity. file:yeast/YDJ1/YDJ1-deep-research-falcon.md Ydj1 stimulates the ATPase activity of yeast Hsp70 (Ssa1), and Ydj1 mutants can show greatly reduced ability to stimulate Hsp70 ATPase activity
GO:0034605 cellular response to heat	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for cellular response to heat is appropriate. YDJ1 is a heat shock gene whose expression increases at elevated temperatures (UniProt). It participates in protein refolding after heat stress as part of the Hsp104/Hsp70/Hsp40 chaperone system (PMID:9674429). Also supported by IMP evidence (PMID:25344756). Reason: YDJ1 is a bona fide heat shock protein involved in stress response. IBA is consistent with IMP evidence and the well-established role of Hsp40 in heat stress response. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001531327 · PANTHER:PTN001531327 SUPPORTS TRANSFER The current PTHR43888 PAINT record places cellular response to heat at this broad eukaryotic J-protein node using fungal and metazoan descendants. Direct YDJ1 heat-stress evidence independently supports the biological assertion.
GO:0042026 protein refolding	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation for protein refolding is well supported. Hsp104, Hsp70 (Ssa1), and Hsp40 (Ydj1) cooperate to refold aggregated proteins (PMID:9674429). YDJ1:Ssa1 can refold luciferase in vitro (PMID:9774392). Reason: Protein refolding is a core biological process for YDJ1 as part of the Hsp104/Hsp70/Hsp40 disaggregation/refolding machinery. Confirmed by IDA (PMID:9674429). Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN001531327 · PANTHER:PTN001531327 SUPPORTS TRANSFER The current PTHR43888 PAINT record places refolding at this broad eukaryotic J-protein node using fungal and metazoan descendants. Direct YDJ1 refolding evidence independently supports the annotation. Supporting Evidence: PMID:9674429 However, in concert with Hsp40 and Hsp70, Hsp104 can reactivate proteins that have been denatured and allowed to aggregate, substrates refractory to the action of other chaperones. PMID:9774392 Ydj1 and Sis1 could both functionally interact with Ssa1, but not the Ssb1/2 proteins, to refold luciferase. Interestingly, Ydj1:Ssa1 could promote up to four times more luciferase folding than Sis1:Ssa1.
GO:0051082 unfolded protein binding	IBA GO_REF:0000033	MODIFY	Summary: GO:0051082 is now formally obsolete. YDJ1 both suppresses aggregation of denatured luciferase and assists Ssa1-dependent refolding (PMID:9774392), supporting the two evidence-matched successor activities: unfolded protein holdase activity (GO:0140309) and protein folding chaperone (GO:0044183). Reason: GO:0051082 "unfolded protein binding" is obsolete with GO:0044183 and GO:0140309 as consider terms. YDJ1's directly demonstrated anti-aggregation and productive Ssa1-assisted folding activities justify both evidence-specific replacements. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN001531327 · PANTHER:PTN001531327 SOURCE STALE OR MISSING The current PTHR43888 PAINT record retains this PTN for related J-protein biology, although it no longer carries obsolete GO:0051082. The term-scoping modification is supported directly by YDJ1 assays, which distinguish holdase and folding-chaperone activities. Proposed replacements: protein folding chaperone unfolded protein holdase activity Supporting Evidence: PMID:9774392 Ydj1 was dramatically more effective than Sis1 at suppressing the thermally induced aggregation of luciferase. Paradoxically, Sis1 and Ydj1 could bind similar quantities of chemically denatured luciferase.
GO:0005634 nucleus	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: IBA annotation for nuclear localization. YDJ1 functions in the nucleus as part of the HMC complex regulating HAP1 transcription factor activity (PMID:15102838). Also involved in tRNA import into nucleus (PMID:25853343). Supported by NAS (PMID:15102838). Reason: Nuclear localization is supported by its role in the HAP1 repressor complex and tRNA nuclear import. It is retained as non-core because YDJ1 is predominantly cytosolic. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN001180221 · PANTHER:PTN001180221 SUPPORTS TRANSFER The current PTHR43888 PAINT record places nucleus at this fungal J-protein node using S. pombe and APJ1 descendants; APJ1 is a class-A/type-I Ydj1 paralog, not Sis1. YDJ1's HAP1 and tRNA-import roles independently make a secondary nuclear pool plausible, although nucleus is not its principal site.
GO:0001671 ATPase activator activity	IEA GO_REF:0000117	ACCEPT	Summary: IEA annotation for ATPase activator activity from ARBA machine learning. Consistent with IDA and IBA evidence for the same term. Reason: Correct IEA annotation. ATPase activator activity is the core molecular function of YDJ1, confirmed by multiple experimental studies (PMID:1400408, PMID:15342786).
GO:0005524 ATP binding	IEA GO_REF:0000002	REMOVE	Summary: IEA annotation for ATP binding based on InterPro domain IPR012724 (DnaJ). While YDJ1 stimulates the ATPase of Hsp70 and regulates substrate binding in an ATP-dependent manner, the ATP binding is a property of Hsp70 (Ssa1), not YDJ1 itself. YDJ1 does not have an intrinsic ATPase or ATP-binding domain. Reason: YDJ1 regulates Hsp70 ATPase activity but does not itself bind ATP. The InterPro mapping appears to be overly broad. The J-domain stimulates ATP hydrolysis by Hsp70 but the DnaJ protein itself is not an ATPase or ATP-binding protein. Family-level review of IPR012724 (Chaperone DnaJ) independently finds this InterPro2GO ATP binding mapping to be factually incorrect for J-domain proteins, as ATP binding/hydrolysis is a property of the Hsp70 partner. Supporting Evidence: file:interpro/interpro/IPR012724/IPR012724-deep-research-falcon.md no evidence supports universal ATP binding by DnaJ family members matched by this InterPro family
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: IEA annotation for cytoplasm based on UniProt subcellular location. Correct but less specific than cytosol (GO:0005829) which is supported by IDA evidence. Reason: Cytoplasm is a correct broader localization, consistent with the more specific cytosol annotation. The IEA mapping from UniProt subcellular location is accurate.
GO:0006457 protein folding	IEA GO_REF:0000002	ACCEPT	Summary: IEA annotation for protein folding from InterPro. YDJ1 participates in protein folding as a co-chaperone of Hsp70. This is accurate at the BP level. Reason: Protein folding is a core biological process for YDJ1, supported by multiple experimental studies including its role in de novo protein folding (PMID:10567418) and protein refolding (PMID:9674429).
GO:0008270 zinc ion binding	IEA GO_REF:0000043	ACCEPT	Summary: IEA annotation for zinc ion binding based on UniProt keyword. YDJ1 has a well-characterized zinc finger cysteine-rich domain (residues 130-213) with four CXXCXGXG repeats that coordinate two zinc ions. Supported by crystal structure (PMID:14656432). Reason: Zinc binding is structurally confirmed. The zinc finger domain is essential for substrate recognition and chaperone function, distinguishing Type I from Type II Hsp40 proteins. Supporting Evidence: file:yeast/YDJ1/YDJ1-deep-research-falcon.md a client-binding CTD containing a zinc-finger-like / cysteine-rich region
GO:0009408 response to heat	IEA GO_REF:0000002	MODIFY	Summary: IEA annotation for response to heat. YDJ1 is a heat-inducible chaperone gene. This is a broader parent of the more specific IBA/IMP-supported cellular response to heat (GO:0034605). Reason: The broad heat-response assertion is sound, but GO:0034605 is the actionable, experimentally and phylogenetically supported child term already used for YDJ1. Proposed replacements: cellular response to heat
GO:0015031 protein transport	IEA GO_REF:0000043	KEEP AS NON CORE	Summary: IEA annotation for protein transport from UniProt keyword. YDJ1 is involved in protein targeting to the ER (PMID:1473150) and mitochondrial protein import, both of which involve protein transport. Reason: Protein transport is a broad but accurate umbrella for YDJ1's documented ER targeting and mitochondrial precursor-transport contexts. Retain it as non-core rather than replacing it only with GO:0045047, which would erase the mitochondrial aspect; the specific ER-targeting assertion is reviewed separately.
GO:0030544 Hsp70 protein binding	IEA GO_REF:0000002	ACCEPT	Summary: IEA annotation for Hsp70 protein binding from InterPro. YDJ1 physically interacts with Ssa1 (Hsp70) through its J-domain and functionally cooperates with it (PMID:1400408, PMID:9774392). Also interacts with Hsp82 (Hsp90). Reason: Hsp70 binding is a core interaction for YDJ1 as a J-domain co-chaperone. However, this is a binding term and the functional relationship is better captured by GO:0001671 (ATPase activator activity). Acceptable as an IEA.
GO:0031072 heat shock protein binding	IEA GO_REF:0000002	ACCEPT	Summary: IEA annotation for heat shock protein binding from InterPro. YDJ1 binds Hsp70 (Ssa1) and Hsp90 (Hsp82). This is a broader parent of Hsp70 protein binding. Reason: Correct but less specific than GO:0030544 (Hsp70 protein binding). Acceptable as a broad IEA annotation.
GO:0046872 metal ion binding	IEA GO_REF:0000043	ACCEPT	Summary: IEA annotation for metal ion binding from UniProt keyword. YDJ1 binds zinc ions via its cysteine-rich domain. This is a broader parent of GO:0008270 (zinc ion binding). Reason: Correct but less specific than zinc ion binding. Acceptable as a broad IEA annotation.
GO:0048471 perinuclear region of cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: IEA annotation for perinuclear region based on UniProt subcellular location. Consistent with IDA evidence from PMID:1869583 showing YDJ1 is concentrated in a perinuclear ring. Reason: Correct annotation supported by experimental evidence. UniProt notes YDJ1 is concentrated in a perinuclear ring as well as in the cytoplasm.
GO:0051082 unfolded protein binding	IEA GO_REF:0000002	MODIFY	Summary: IEA annotation for unfolded protein binding from InterPro. GO:0051082 is obsolete; direct YDJ1 experiments distinguish both anti-aggregation holdase activity and Ssa1-assisted protein folding chaperone activity. Reason: Replace the obsolete binding term with both evidence-matched activities demonstrated for YDJ1, rather than choosing one successor from the InterPro mapping alone. Proposed replacements: protein folding chaperone unfolded protein holdase activity
GO:0005515 protein binding	IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy...	MARK AS OVER ANNOTATED	Summary: IPI annotation for protein binding from large-scale mass spectrometry identification of protein complexes. IntAct records interactions with RAD3, RAD24, and CTR9. Reason: Protein binding (GO:0005515) is uninformative. The relevant interactions are better captured by more specific terms like Hsp70 protein binding (GO:0030544) or protein-folding chaperone binding (GO:0051087). Large-scale studies often detect indirect associations.
GO:0005515 protein binding	IPI PMID:15879519 A two-hybrid screen of the yeast proteome for Hsp90 interact...	MARK AS OVER ANNOTATED	Summary: IPI annotation for protein binding from two-hybrid screen for Hsp90 interactors. IntAct records interaction with HSP82 (P02829). Reason: Protein binding is uninformative. The YDJ1-Hsp90 interaction is functionally relevant (co-chaperone relationship) but better captured by heat shock protein binding (GO:0031072).
GO:0005515 protein binding	IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine...	MARK AS OVER ANNOTATED	Summary: IPI annotation for protein binding from proteome survey. IntAct records interaction with RAD3. Reason: Protein binding is uninformative for a chaperone/co-chaperone protein that interacts with many substrates and partners.
GO:0005515 protein binding	IPI PMID:17441508 SGT2 and MDY2 interact with molecular chaperone YDJ1 in Sacc...	MARK AS OVER ANNOTATED	Summary: IPI annotation for protein binding showing YDJ1 interaction with SGT2 and MDY2. These are components of the TRC/GET pathway for tail-anchored protein insertion. Reason: Protein binding is uninformative. The interaction with SGT2 and MDY2 is functionally relevant to YDJ1's role in the TRC complex (GO:0072380) for tail-anchored protein targeting.
GO:0005515 protein binding	IPI PMID:18833196 Hsp104, Hsp70 and Hsp40 interplay regulates formation, growt...	MARK AS OVER ANNOTATED	Summary: IPI annotation for protein binding showing interaction with SUP35 (Q7LKB1, a prion protein). Part of the Hsp104/Hsp70/Hsp40 system regulating prion formation. Reason: Protein binding is uninformative. The interaction with SUP35 reflects YDJ1's chaperone function in prion regulation.
GO:0005515 protein binding	IPI PMID:19536198 An atlas of chaperone-protein interactions in Saccharomyces ...	MARK AS OVER ANNOTATED	Summary: IPI annotation for protein binding from atlas of chaperone-protein interactions. IntAct records multiple interactions including HSP82, RAD3, SSA1, SSE1, and others. Reason: Protein binding is uninformative for a co-chaperone. The interactions with Ssa1 (Hsp70) and Hsp82 (Hsp90) are better captured by specific binding terms.
GO:0005515 protein binding	IPI PMID:23217712 CDK-dependent Hsp70 Phosphorylation controls G1 cyclin abund...	MARK AS OVER ANNOTATED	Summary: IPI annotation for protein binding showing interaction with SSA1 (P10591). CDK-dependent phosphorylation of Hsp70 regulates G1 cyclin abundance. Reason: Protein binding is uninformative. The Ssa1 interaction is the core functional partnership of YDJ1 as a J-domain co-chaperone.
GO:0005515 protein binding	IPI PMID:37968396 The social and structural architecture of the yeast protein ...	MARK AS OVER ANNOTATED	Summary: IPI annotation for protein binding from social and structural architecture of yeast protein interactome. IntAct records interactions with TIF2, EFT2, and SSE1. Reason: Protein binding is uninformative for a co-chaperone that interacts broadly with substrates and partner chaperones.
GO:0005634 nucleus	NAS PMID:15102838 A novel mode of chaperone action - heme activation of Hap1 b...	KEEP AS NON CORE	Summary: NAS annotation for nuclear localization from ComplexPortal, based on YDJ1 function in the HMC complex that regulates HAP1 transcription factor (PMID:15102838). YDJ1 is part of the Hsp70-Ydj1 complex that represses HAP1 activity in the absence of heme. Reason: Nuclear localization is supported by YDJ1's role in the HAP1 repressor complex. Consistent with IBA evidence for the same term, but secondary to its predominant cytosolic localization.
GO:0045892 negative regulation of DNA-templated transcription	NAS PMID:15102838 A novel mode of chaperone action - heme activation of Hap1 b...	KEEP AS NON CORE	Summary: NAS annotation from ComplexPortal. YDJ1 is part of the HMC complex that represses HAP1 transcriptional activity in the absence of heme (PMID:15102838, PMID:11689685). Reason: YDJ1 participates in transcriptional repression of HAP1 as part of the Hsp70-Ydj1 chaperone complex, but this is a secondary function. The primary role of YDJ1 is as a co-chaperone, and the transcriptional regulatory effect is a consequence of its chaperoning of HAP1.
GO:0070482 response to oxygen levels	NAS PMID:15102838 A novel mode of chaperone action - heme activation of Hap1 b...	KEEP AS NON CORE	Summary: NAS annotation from ComplexPortal. YDJ1 mediates heme-dependent regulation of HAP1, which is a heme-responsive transcription factor that senses oxygen/heme levels (PMID:15102838). Reason: YDJ1's role in oxygen response is indirect, through its chaperone function in the HAP1 regulatory complex. It is not an oxygen sensor itself.
GO:0070482 response to oxygen levels	NAS PMID:9632766 Molecular mechanism governing heme signaling in yeast - a hi...	KEEP AS NON CORE	Summary: NAS annotation from ComplexPortal. Same biological role as above - YDJ1 participates in the higher-order complex mediating heme regulation of HAP1 (PMID:9632766). Reason: Duplicate biological process annotation with different reference. YDJ1's role in oxygen response is through the HAP1 chaperone complex, not a direct sensory function.
GO:0009267 cellular response to starvation	IMP PMID:25853343 Cytosolic Hsp70 and co-chaperones constitute a novel system ...	KEEP AS NON CORE	Summary: IMP annotation for cellular response to starvation. PMID:25853343 describes YDJ1's role in tRNA import into the nucleus, which is involved in the starvation response. Reason: Cellular response to starvation is a downstream phenotypic consequence of YDJ1's co-chaperone function in tRNA nuclear import. Not a core function of YDJ1.
GO:0034605 cellular response to heat	IMP PMID:25344756 Rsp5/Nedd4 is the main ubiquitin ligase that targets cytosol...	ACCEPT	Summary: IMP annotation for cellular response to heat. YDJ1 is a heat-inducible co-chaperone that participates in the heat stress response through protein refolding and quality control. Reason: Cellular response to heat is a core biological process for YDJ1. It is induced by heat stress and functions in the Hsp104/Hsp70/Hsp40 refolding system. Supporting Evidence: PMID:25344756 We found that ubiquitylation of heat-induced substrates requires the Hsp40 co-chaperone Ydj1 that is further associated with Rsp5 upon heat shock.
GO:0036503 ERAD pathway	IMP PMID:15252059 Distinct machinery is required in Saccharomyces cerevisiae f...	ACCEPT	Summary: IMP annotation for ERAD pathway. YDJ1 is required for efficient ERAD of both soluble luminal and multispanning membrane ERAD substrates (PMID:15252059). Reason: ERAD is a well-documented function of YDJ1. As a cytosolic co-chaperone, YDJ1 assists in the retrotranslocation and degradation of misfolded ER proteins.
GO:0036503 ERAD pathway	IMP PMID:15342786 Distinct roles for the Hsp40 and Hsp90 molecular chaperones ...	ACCEPT	Summary: IMP annotation for ERAD pathway. YDJ1 plays distinct roles from Hsp90 in CFTR degradation in yeast (PMID:15342786). YDJ1 stimulates Ssa1 ATPase activity to promote CFTR degradation. Reason: Additional evidence supporting YDJ1's role in ERAD, specifically for CFTR degradation. Consistent with the other ERAD annotation.
GO:0008270 zinc ion binding	RCA PMID:30358795 The cellular economy of the Saccharomyces cerevisiae zinc pr...	ACCEPT	Summary: RCA annotation for zinc ion binding from analysis of the yeast zinc proteome. Consistent with the known zinc finger domain (residues 130-213) with four CXXCXGXG repeats coordinating two Zn2+ ions. Reason: Zinc binding is structurally confirmed by crystal structure (PMID:14656432). The RCA annotation is well supported.
GO:0005829 cytosol	HDA PMID:26928762 One library to make them all - streamlining the creation of ...	ACCEPT	Summary: HDA annotation for cytosol localization from large-scale yeast library creation and analysis (PMID:26928762). Consistent with IDA evidence. Reason: High-throughput data supporting cytosol localization. Consistent with targeted IDA studies (PMID:1869583, PMID:8144572).
GO:0006511 ubiquitin-dependent protein catabolic process	IMP PMID:25344756 Rsp5/Nedd4 is the main ubiquitin ligase that targets cytosol...	KEEP AS NON CORE	Summary: IMP annotation for ubiquitin-dependent protein catabolic process. YDJ1 participates in ubiquitin-dependent degradation of misfolded or damaged proteins, particularly during heat stress. Reason: YDJ1 facilitates ubiquitin-dependent degradation as part of its co-chaperone function in protein quality control. This is a downstream consequence of its chaperone activity rather than a direct enzymatic function.
GO:0051131 chaperone-mediated protein complex assembly	IDA PMID:10811660 Crystal structure and activity of human p23, a heat shock pr...	MARK AS OVER ANNOTATED	Summary: This CAFA-assigned IDA has empty WITH/FROM and cites an abstract-only human p23 study. The abstract demonstrates p23 chaperoning of progesterone receptor but provides no direct YDJ1 assay. Reason: Chaperone-mediated assembly is broadly compatible with Ydj1 biology, but CAFA's IDA transfers a process from a different human Hsp90 cochaperone without documented YDJ1 evidence or a source entity. The row therefore overstates direct experimental support. This is not treated as MOD-curated evidence, and no wrong-identifier claim is made beyond what the cached abstract shows.
GO:0035719 tRNA import into nucleus	IMP PMID:25853343 Cytosolic Hsp70 and co-chaperones constitute a novel system ...	KEEP AS NON CORE	Summary: IMP annotation for tRNA import into nucleus. Cytosolic Hsp70 and its co-chaperones (including YDJ1) constitute a novel system for tRNA import into the nucleus (PMID:25853343). Reason: tRNA nuclear import is a specific function of the Hsp70-YDJ1 co-chaperone system but is not the core molecular function of YDJ1. It represents a specialized application of its general co-chaperone activity.
GO:0001671 ATPase activator activity	IDA PMID:1400408 Regulation of Hsp70 function by a eukaryotic DnaJ homolog.	ACCEPT	Summary: IDA annotation for ATPase activator activity. This is the foundational paper demonstrating that YDJ1p stimulates the ATPase activity of Hsp70 Ssa1 (PMID:1400408). Reason: Core molecular function of YDJ1, demonstrated by direct biochemical assay. Supporting Evidence: PMID:1400408 We report that a purified cytoplasmic Hsp70 homolog from Saccharomyces cerevisiae, Hsp70SSA1, exhibits a weak ATPase activity, which is stimulated by a purified eukaryotic dnaJp homolog (YDJ1p).
GO:0001671 ATPase activator activity	IDA PMID:15342786 Distinct roles for the Hsp40 and Hsp90 molecular chaperones ...	ACCEPT	Summary: IDA annotation for ATPase activator activity from study of Hsp40/Hsp90 roles in CFTR degradation. YDJ1 stimulates Ssa1 ATPase activity in the context of ERAD. Reason: Additional experimental evidence confirming ATPase activator activity, the core molecular function of YDJ1.
GO:0005829 cytosol	IDA PMID:1869583 Characterization of YDJ1 - a yeast homologue of the bacteria...	ACCEPT	Summary: IDA annotation for cytosol localization from the original characterization of YDJ1 by immunofluorescence (PMID:1869583). Reason: Primary experimental evidence for cytosol localization from the founding characterization paper.
GO:0005829 cytosol	IDA PMID:8144572 Differential regulation of Hsp70 subfamilies by the eukaryot...	ACCEPT	Summary: IDA annotation for cytosol localization from differential regulation study of Hsp70 subfamilies by YDJ1 (PMID:8144572). Reason: Additional experimental evidence for cytosol localization.
GO:0006458 'de novo' protein folding	IMP PMID:10567418 Mutations in the yeast Hsp40 chaperone protein Ydj1 cause de...	ACCEPT	Summary: IMP annotation for de novo protein folding. Mutations in YDJ1 cause defects in Axl1 biogenesis and pro-alpha-factor processing (PMID:10567418), indicating a role in de novo folding of newly synthesized proteins. Reason: De novo protein folding is a core biological process for YDJ1. As a co-chaperone of Hsp70, YDJ1 assists in folding newly synthesized polypeptides.
GO:0042026 protein refolding	IDA PMID:9674429 Hsp104, Hsp70, and Hsp40 - a novel chaperone system that res...	ACCEPT	Summary: IDA annotation for protein refolding. Hsp104, Hsp70, and Hsp40 (YDJ1) cooperate to rescue previously aggregated proteins (PMID:9674429). Reason: Protein refolding is a core biological process for YDJ1. Direct assay evidence from the landmark Glover and Lindquist paper. Supporting Evidence: PMID:9674429 However, in concert with Hsp40 and Hsp70, Hsp104 can reactivate proteins that have been denatured and allowed to aggregate, substrates refractory to the action of other chaperones.
GO:0045047 protein targeting to ER	IMP PMID:1473150 YDJ1p facilitates polypeptide translocation across different...	ACCEPT	Summary: IMP annotation for protein targeting to ER. YDJ1 is required for efficient translocation of pre-pro-alpha-factor across the ER membrane (PMID:1473150). Reason: Protein targeting to ER is a well-established function of YDJ1, originally identified through its role in maintaining translocation competence of precursor proteins. Supporting Evidence: file:yeast/YDJ1/YDJ1-deep-research-falcon.md conditional YDJ1 mutants showed defective import of multiple substrates into mitochondria and defective translocation of an ER substrate at the restrictive temperature, supporting that Ydj1 facilitates translocation across both mitochondrial and ER membranes
GO:0048471 perinuclear region of cytoplasm	IDA PMID:1869583 Characterization of YDJ1 - a yeast homologue of the bacteria...	ACCEPT	Summary: IDA annotation for perinuclear region of cytoplasm. YDJ1 is concentrated in a perinuclear ring by immunofluorescence (PMID:1869583). Reason: Primary experimental evidence for perinuclear localization from the founding characterization paper.
GO:0051082 unfolded protein binding	IDA PMID:9774392 Protein folding activity of Hsp70 is modified differentially...	MODIFY	Summary: IDA annotation based on direct luciferase assays. YDJ1 bound chemically denatured luciferase, suppressed thermal aggregation, and with Ssa1 promoted refolding (PMID:9774392), directly distinguishing holdase and folding-chaperone activities. Reason: GO:0051082 is obsolete. The anti-aggregation assay supports GO:0140309, while the productive Ssa1-dependent refolding assay supports GO:0044183; both replacements are warranted by this reference. Proposed replacements: protein folding chaperone unfolded protein holdase activity Supporting Evidence: PMID:9774392 Ydj1 was dramatically more effective than Sis1 at suppressing the thermally induced aggregation of luciferase. Paradoxically, Sis1 and Ydj1 could bind similar quantities of chemically denatured luciferase. file:yeast/YDJ1/YDJ1-deep-research-falcon.md Ydj1 is an Hsp70 co-chaperone that presents unfolded or non-native clients to Hsp70 and promotes productive folding/triage via J-domain–stimulated Hsp70 ATP hydrolysis
GO:0072380 TRC complex	IDA PMID:20850366 A chaperone cascade sorts proteins for posttranslational mem...	MARK AS OVER ANNOTATED	Summary: The cited study establishes a sequential tail-anchored-protein chaperone cascade. Ydj1/Ssa1 act upstream in client handling, whereas GO:0072380 denotes the Get4-Get5/Mdy2 TRC complex. Reason: Participation in upstream handoff does not establish that Ydj1 is a stable part of TRC. Retain the pathway connection but mark the complex-membership assertion over-annotated; direct stoichiometric incorporation would be needed. Supporting Evidence: PMID:20850366 Thus, ER-bound TA proteins are sorted at the top of a TMD chaperone cascade that culminates with the formation of Get3-TA protein complexes, which are recruited to the ER membrane for insertion.

Gene Description

Existing Annotations Review

Core Functions

Hsp40/DnaJ co-chaperone that stimulates ATPase activity of Hsp70 (Ssa1) and delivers substrate proteins for folding. Functions in protein refolding with Hsp104/Hsp70, de novo protein folding, ERAD, and protein targeting to ER.

Protein folding chaperone activity - binds unfolded/denatured substrates via C-terminal peptide-binding domain and zinc finger region, delivering them to Hsp70 for folding.

Unfolded protein holdase activity - directly suppresses aggregation of non-native clients before their productive transfer into the Ssa1 folding cycle.

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

Falcon

📚 Additional Documentation

Notes

📄 View Raw YAML