Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping
Electronic Gene Ontology annotations created by ARBA machine learning models
InterPro family deep research on IPR012724 (Chaperone DnaJ)
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Family-level review of the Chaperone DnaJ (IPR012724) signature finds the InterPro2GO GO:0005524 (ATP binding) mapping factually incorrect, because ATP binding/hydrolysis is a property of the Hsp70 partner and J-domain proteins lack an ATP-binding pocket.
"no evidence supports universal ATP binding by DnaJ family members matched by this InterPro family"
Falcon deep research report on YDJ1 (Saccharomyces cerevisiae)
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YDJ1/MAS5 is the S. cerevisiae cytosolic DnaJ/Hsp40 J-domain co-chaperone that
presents non-native clients to Hsp70 and stimulates Hsp70 (Ssa1) ATPase activity
through its J-domain HPD motif, driving client folding, transfer and triage. This
is the core molecular function and the basis for the GO:0001671 ATPase activator
activity annotation.
"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"
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Ydj1 stimulates the ATPase activity of yeast Hsp70 (Ssa1), and loss-of-function
Ydj1 mutants are greatly impaired for Hsp70 ATPase stimulation, confirming ATPase
activator activity (GO:0001671) by direct biochemistry.
"Ydj1 stimulates the ATPase activity of yeast Hsp70 (Ssa1), and Ydj1 mutants can show greatly reduced ability to stimulate Hsp70 ATPase activity"
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Classic conditional YDJ1 mutants are defective for import of multiple substrates
into mitochondria and for translocation of an ER substrate at restrictive
temperature, establishing that Ydj1 facilitates precursor translocation across both
mitochondrial and ER membranes (supports protein targeting to ER GO:0045047 and
protein transport GO:0015031).
"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"
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Cytosolic Hsp70s and Hsp40s including Ydj1 physically interact with newly
synthesized mitochondrial beta-barrel precursors and their depletion reduces
beta-barrel import, coupling Ydj1 to TOM/Tom70-dependent mitochondrial import.
"including Ydj1 and Sis1 physically interact with newly synthesized mitochondrial β-barrel precursors"
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Ydj1 is predominantly cytosolic but partially membrane-associated via C-terminal
farnesylation, and is found at the cytosol, ER, and mitochondrial membranes,
consistent with cytosol (GO:0005829) and perinuclear/ER membrane localization.
"Ydj1 is predominantly **cytosolic**, but is **partially membrane-associated** through its C-terminal prenylation (farnesylation)"
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Review and experimental evidence place Ydj1 in the cytosol, ER/perinuclear
membrane, and mitochondrial membranes, consistent with its organellar protein
targeting roles.
"A review specifically places Ydj1 in the **cytosol, ER, and mitochondrial membranes**"
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Ydj1 is a type-I Hsp40 with an N-terminal J-domain, a G/F-rich region linked to
client specificity, and a client-binding C-terminal domain containing a
zinc-finger-like / cysteine-rich region, supporting zinc ion binding (GO:0008270).
"a client-binding CTD containing a **zinc-finger-like / cysteine-rich region**"
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Ydj1 is a CaaX protein (C-terminal motif CASQ) that is farnesylated by FTase;
farnesylation is required for optimal growth at elevated temperature, supporting
its role at organelle membranes and in thermotolerance.
"Ydj1 is a **CaaX protein** whose C-terminal cysteine is prenylated (classically farnesylated by FTase)"
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Ydj1 acts as an Hsp70 co-chaperone that regulates the stability and activity of
ribonucleotide reductase, illustrating that its co-chaperone activity also
stabilizes specific functional enzyme complexes.
"a PLOS Genetics study framed Ydj1 as an Hsp70 co-chaperone that regulates the stability/activity of ribonucleotide reductase (RNR)"
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Ydj1 participates in yeast prion propagation; fibril fragmentation of Sup35NM
amyloid can be aided by either Sis1 or Ydj1, though Ydj1 binds the fibrils with
lower affinity than Sis1.
"fibril fragmentation can be aided by either Sis1 or Ydj1"
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Ydj1 is extremely abundant (>40,000 molecules per cell) and J-domain lysine
acetylation (e.g. K23, K37) fine-tunes Ssa1 binding, ATPase stimulation and client
refolding, representing a regulatory chaperone-code layer.
"Ydj1 is extremely abundant (**>40,000 molecules per cell**) and that **J-domain lysine acetylation** can fine-tune proteostasis and translation-associated functions"
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A 2023 yeast study concluded that Ydj1 and Mdj1 are not critically involved in
Fe/S protein biogenesis or iron regulation, refining the boundaries of Ydj1
functional annotation (a negative/scoping result).
"A yeast study concluded that Ydj1 and Mdj1 are not critically involved in Fe/S protein biogenesis or iron regulation, refining the boundaries of Ydj1 functional annotation"
Mutations in the yeast Hsp40 chaperone protein Ydj1 cause defects in Axl1 biogenesis and pro-a-factor processing.
Crystal structure and activity of human p23, a heat shock protein 90 co-chaperone.
The Hsp70-Ydj1 molecular chaperone represses the activity of the heme activator protein Hap1 in the absence of heme.
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.
Regulation of Hsp70 function by a eukaryotic DnaJ homolog.
The crystal structure of the yeast Hsp40 Ydj1 complexed with its peptide substrate.
YDJ1p facilitates polypeptide translocation across different intracellular membranes by a conserved mechanism.
A novel mode of chaperone action - heme activation of Hap1 by enhanced association of Hsp90 with the repressed Hsp70-Hap1 complex.
Distinct machinery is required in Saccharomyces cerevisiae for the endoplasmic reticulum-associated degradation of a multispanning membrane protein and a soluble luminal protein.
Distinct roles for the Hsp40 and Hsp90 molecular chaperones during cystic fibrosis transmembrane conductance regulator degradation in yeast.
A two-hybrid screen of the yeast proteome for Hsp90 interactors uncovers a novel Hsp90 chaperone requirement in the activity of a stress-activated mitogen-activated protein kinase, Slt2p (Mpk1p).
Proteome survey reveals modularity of the yeast cell machinery.
SGT2 and MDY2 interact with molecular chaperone YDJ1 in Saccharomyces cerevisiae.
Characterization of YDJ1 - a yeast homologue of the bacterial dnaJ protein.
Hsp104, Hsp70 and Hsp40 interplay regulates formation, growth and elimination of Sup35 prions.
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell.
A chaperone cascade sorts proteins for posttranslational membrane insertion into the endoplasmic reticulum.
CDK-dependent Hsp70 Phosphorylation controls G1 cyclin abundance and cell-cycle progression.
Rsp5/Nedd4 is the main ubiquitin ligase that targets cytosolic misfolded proteins following heat stress.
Cytosolic Hsp70 and co-chaperones constitute a novel system for tRNA import into the nucleus.
One library to make them all - streamlining the creation of yeast libraries via a SWAp-Tag strategy.
The cellular economy of the Saccharomyces cerevisiae zinc proteome.
The social and structural architecture of the yeast protein interactome.
Differential regulation of Hsp70 subfamilies by the eukaryotic DnaJ homologue YDJ1.
Molecular mechanism governing heme signaling in yeast - a higher-order complex mediates heme regulation of the transcriptional activator HAP1.
Hsp104, Hsp70, and Hsp40 - a novel chaperone system that rescues previously aggregated proteins.
Protein folding activity of Hsp70 is modified differentially by the hsp40 co-chaperones Sis1 and Ydj1.
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YDJ1 suppresses thermally induced aggregation of luciferase
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YDJ1:Ssa1 promotes up to four times more luciferase refolding than Sis1:Ssa1
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YDJ1 contains a zinc finger region absent from Sis1 that enhances chaperone function
Deep research report on YDJ1 (Falcon/Edison Scientific Literature)
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YDJ1 is the type I cytosolic Hsp40/J-domain co-chaperone of Saccharomyces cerevisiae (paralogous to Sis1 type II), comprising an N-terminal J-domain that stimulates Hsp70 (Ssa1) ATPase activity, a glycine/phenylalanine-rich region, a zinc-finger / peptide-binding cleft module, and a C-terminal dimerization domain; YDJ1 is farnesylated at its C-terminal CAAX box and recruits to ER and other membranes via this lipid anchor.
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YDJ1 has broad roles in cytosolic and ER-targeted protein folding, chaperone-mediated ribosome-associated quality control, and protein refolding from aggregates via the Hsp104-Hsp70-YDJ1 system; the YDJ1/Ssa1 pair outperforms Sis1/Ssa1 in luciferase refolding by approximately 4-fold, consistent with the zinc-finger enhancing chaperone selectivity for misfolded substrates.