DnaJ

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005737 cytoplasm	IBA GO_REF:0000033	ACCEPT	Summary: DnaJ is a cytoplasmic protein in E. coli. The IBA annotation is consistent with experimental IDA evidence from PMID:6220698 and UniProt subcellular location annotation. Zylicz et al. (1983) identified DnaJ in minicells and showed it has membrane affinity but is primarily cytoplasmic. Reason: Well-supported by phylogenetic inference and consistent with direct experimental evidence (IDA from PMID:6220698) and UniProt subcellular location (Cytoplasm). Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN002454318 · PANTHER:PTN002454318 SUPPORTS TRANSFER Current PTHR43096 PAINT retains GO:0005737 at this node. PomBase:SPBC11B10.05c · PomBase:SPBC11B10.05c SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. SGD:S000001878 · SGD:S000001878 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. TAIR:locus:2016234 · TAIR:locus:2016234 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. TAIR:locus:2041258 · TAIR:locus:2041258 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. TAIR:locus:2088585 · TAIR:locus:2088585 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. TAIR:locus:2140035 · TAIR:locus:2140035 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. TAIR:locus:2162692 · TAIR:locus:2162692 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. TAIR:locus:2172374 · TAIR:locus:2172374 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. TAIR:locus:2174239 · TAIR:locus:2174239 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. UniProtKB:P08622 · DnaJ SUPPORTS TRANSFER DnaJ's own experimental localization is valid descendant evidence, not circular propagation. UniProtKB:Q38EC6 · UniProtKB:Q38EC6 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. UniProtKB:Q4GZ96 · UniProtKB:Q4GZ96 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. UniProtKB:Q583X4 · UniProtKB:Q583X4 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. Supporting Evidence: PMID:6220698 Escherichia coli dnaJ- and dnaK-gene products have been identified in a system of minicells infected with the appropriate transducing lambda phages.
GO:0042026 protein refolding	IBA GO_REF:0000033	ACCEPT	Summary: DnaJ participates in protein refolding as part of the DnaK/DnaJ/GrpE chaperone system. The IBA annotation is well-supported by experimental evidence showing DnaJ involvement in refolding denatured substrates (PMID:7559385, PMID:20953191). Reason: Core function of DnaJ. The DnaK/DnaJ/GrpE system refolds misfolded proteins, and DnaJ is essential for substrate delivery and DnaK activation in this process. Supported by IDA from PMID:7559385 and the unfoldase/refolding work of PMID:20953191. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN002454318 · PANTHER:PTN002454318 SUPPORTS TRANSFER Current PTHR43096 PAINT retains GO:0042026 at this node. SGD:S000001878 · SGD:S000001878 SUPPORTS TRANSFER Listed descendant evidence supporting ancestral refolding involvement. UniProtKB:P08622 · DnaJ SUPPORTS TRANSFER DnaJ's own experimental refolding annotation is valid descendant evidence and supports the node placement. Supporting Evidence: PMID:7559385 The DnaJ protein of Escherichia coli and the DnaJ-like proteins of eukaryotes are known as molecular chaperones and specific regulators of DnaK-like proteins and are involved in protein folding and renaturation after stress. PMID:20953191 Hsp70-Hsp40-NEF and possibly Hsp100 are the only known molecular chaperones that can use the energy of ATP to convert stably pre-aggregated polypeptides into natively refolded proteins.
GO:0051082 unfolded protein binding	IBA GO_REF:0000033	MODIFY	Summary: DnaJ does bind unfolded proteins via its C-terminal domain and delivers them to DnaK. However, GO:0051082 "unfolded protein binding" is now formally obsolete, and DnaJ is better described as a protein folding chaperone (GO:0044183) since its binding to unfolded proteins is in the context of the chaperone folding cycle, not as an independent binding function. DnaJ is a co-chaperone, not an independent foldase. Reason: GO:0051082 is now formally obsolete. DnaJ binds unfolded substrates as part of the DnaK/DnaJ/GrpE chaperone cycle, not as an independent unfolded-protein binder. GO:0044183 "protein folding chaperone" better captures this co-chaperone function. Note that GO:0003767 "co-chaperone activity" is obsolete, so GO:0044183 is the pragmatic interim term. Propagation Review Root cause: SOURCE STALE OR MISSING Sources checked: PANTHER:PTN002454318 · PANTHER:PTN002454318 SOURCE STALE OR MISSING Current PTHR43096 PAINT retains cytoplasm and protein-refolding assertions at this node, but no GO:0051082 assertion. SGD:S000001878 · SGD:S000001878 SOURCE STALE OR MISSING This protein occurs in the historical WITH/FROM, but the current GO:0051082 node assertion is absent. UniProtKB:P08622 · DnaJ SOURCE STALE OR MISSING DnaJ occurs in the historical WITH/FROM, but the current PAINT assertion is absent. Direct DnaJ evidence supports the replacement term, not a current propagation claim. Proposed replacements: protein folding chaperone Supporting Evidence: PMID:12941935 it appears that zinc center II mutant proteins lack a necessary additional interaction site with DnaK, which seems to be crucial for locking-in substrate proteins onto DnaK. file:ECOLI/DnaJ/DnaJ-deep-research-falcon.md DnaJ binds partially/unfolded substrate
GO:0045892 negative regulation of DNA-templated transcription	IEA GO_REF:0000108	ACCEPT	Summary: This IEA annotation is logically inferred from the sigma factor antagonist activity annotation (GO:0016989). DnaJ, together with DnaK, inactivates sigma32 by direct binding, thereby negatively regulating heat shock gene transcription (PMID:8599944, PMID:1534276). The inference is sound. Reason: Logical inference from GO:0016989 sigma factor antagonist activity. DnaJ binds sigma32 directly and cooperates with DnaK to inhibit its transcriptional activity, constituting negative regulation of transcription (PMID:8599944). Supporting Evidence: PMID:8599944 DnaK and DnaJ cooperatively inhibit sigma32 activity in heat shock gene transcription and GrpE partially reverses this inhibition.
GO:0005524 ATP binding	IEA GO_REF:0000002	REMOVE	Summary: IEA from InterPro mapping (IPR012724, the DnaJ family). However, DnaJ itself does not bind or hydrolyze ATP. DnaJ stimulates the ATPase activity of DnaK, but the ATP binding is by DnaK, not DnaJ. The InterPro mapping is incorrect for DnaJ specifically. Reason: DnaJ does not bind ATP. It stimulates the ATPase activity of DnaK (the Hsp70), which is the ATP-binding partner. UniProt does not list ATP binding as a feature of DnaJ, and no experimental evidence supports direct ATP binding by DnaJ. This is an erroneous IEA mapping from the DnaJ family InterPro entry. Supporting Evidence: PMID:8599944 DnaJ, through rapid association with sigma32 and stimulation of hydrolysis of DnaK-bound ATP, mediates efficient binding of DnaK to sigma32 in the presence of ATP
GO:0005737 cytoplasm	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation from UniProt subcellular location mapping. Consistent with experimental IDA evidence (PMID:6220698) and IBA annotation. DnaJ is a cytoplasmic protein. Reason: Correctly maps UniProt subcellular location annotation. Redundant with but consistent with the IBA and IDA annotations for the same term.
GO:0006260 DNA replication	IEA GO_REF:0000043	KEEP AS NON CORE	Summary: IEA from UniProt keyword mapping (KW-0235 "DNA replication"). The attached literature establishes DnaJ participation in phage lambda genome replication as part of the DnaK/DnaJ/GrpE chaperone system, which remodels the replication initiation complex (PMID:1361234, PMID:3889001). This is a specialized non-core application of DnaJ's chaperone activity. Reason: DnaJ involvement in DNA replication is indirect -- it functions as a chaperone to disassemble replication initiation complexes (e.g., lambda P protein release from the preprimosomal complex). This is a downstream application of its chaperone activity, not a core biochemical function. Supported by PMID:1361234 and PMID:2144273. Supporting Evidence: PMID:1361234 a set of Escherichia coli heat shock proteins termed the Hsp70 complex--DnaK, DnaJ, and GrpE--act with ATP to release lambda P protein from the nucleo-protein complex, freeing the DnaB helicase for its DNA-unwinding reaction.
GO:0006457 protein folding	IEA GO_REF:0000002	ACCEPT	Summary: IEA from InterPro mapping. DnaJ participates in protein folding as part of the DnaK/DnaJ/GrpE chaperone system. This is a core biological process annotation. Reason: Protein folding is a core biological process for DnaJ. Consistent with DnaJ-specific experimental evidence from PMID:7559385.
GO:0008270 zinc ion binding	IEA GO_REF:0000120	ACCEPT	Summary: IEA from UniProt keyword/rule mapping. DnaJ binds 2 Zn(2+) ions per monomer via its cysteine-rich zinc finger domain (residues 131-209). Well-supported by experimental evidence (PMID:8662861, PMID:11732919, PMID:12941935). Reason: Zinc binding is a well-established structural feature of DnaJ. UniProt documents 8 zinc-coordinating cysteine residues. Consistent with multiple IDA annotations.
GO:0009408 response to heat	IEA GO_REF:0000002	ACCEPT	Summary: IEA from InterPro mapping. DnaJ is a heat shock protein induced by heat stress under control of the HtpR regulatory protein. It participates in the heat shock response both as a chaperone that refolds denatured proteins and as a regulator of sigma32. Reason: Well-supported. DnaJ is a classic heat shock protein (HSP40). Consistent with IMP from PMID:2144273 and IEP from PMID:8349564. Supporting Evidence: PMID:2144273 dnaJ-insertion mutants did not grow as well as the wild type at temperatures above 30 degrees C
GO:0031072 heat shock protein binding	IEA GO_REF:0000002	MODIFY	Summary: IEA from InterPro (IPR001305, the DnaJ cysteine-rich domain). DnaJ directly binds DnaK (Hsp70) via its J-domain and zinc finger region. This is well-established experimentally (PMID:9860950, PMID:10521435, PMID:22065753). However, the term "heat shock protein binding" is quite vague. The more specific GO:0051087 "protein-folding chaperone binding" is supported by multiple correctly cited DnaJ-DnaK IPI rows. Reason: The mapping reflects the core DnaJ-DnaK interaction, but heat shock protein binding is unnecessarily broad. GO:0051087 specifically captures binding to the protein-folding chaperone DnaK. Proposed replacements: protein-folding chaperone binding
GO:0046872 metal ion binding	IEA GO_REF:0000043	MODIFY	Summary: IEA from UniProt keyword mapping (KW-0479 "Metal-binding"). DnaJ binds zinc ions. This is a broad parent term; the more specific GO:0008270 "zinc ion binding" is already annotated with IDA evidence. Reason: The keyword mapping is directionally correct but unnecessarily general; DnaJ specifically binds two Zn(2+) ions per monomer. GO:0008270 is supported by multiple experimental annotations. Proposed replacements: zinc ion binding
GO:0051082 unfolded protein binding	IEA GO_REF:0000120	MODIFY	Summary: IEA from combined automated annotation. DnaJ binds unfolded substrates via its C-terminal domain, but this binding is in the context of the chaperone cycle. Same reasoning as the IBA annotation for GO:0051082 -- should be modified to GO:0044183. Reason: GO:0051082 is now formally obsolete. DnaJ binds unfolded proteins as part of its co-chaperone function in the DnaK/DnaJ/GrpE folding cycle. GO:0044183 "protein folding chaperone" is the appropriate interim replacement. Proposed replacements: protein folding chaperone
GO:0005515 protein binding	IPI PMID:10521435 Structural features required for the interaction of the Hsp7...	MODIFY	Summary: IPI with DnaK (P0A6Y8). Demonstrates structural features required for DnaK-DnaJ interaction. DnaJ binds DnaK via its J-domain (stimulating ATPase) and zinc finger region (locking substrates onto DnaK). This is better captured by GO:0051087 "protein-folding chaperone binding", supported by multiple correctly cited DnaJ-DnaK interaction studies. Reason: "Protein binding" is uninformative per curation guidelines. The interaction with DnaK is specifically a chaperone-cochaperone interaction. GO:0051087 "protein-folding chaperone binding" is supported for this interaction by the DnaJ-specific study PMID:10521435 and is the appropriate specific term. Proposed replacements: protein-folding chaperone binding Supporting Evidence: PMID:10521435 Structural features required for the interaction of the Hsp70 molecular chaperone DnaK with its cochaperone DnaJ.
GO:0005515 protein binding	IPI PMID:15690043 Interaction network containing conserved and essential prote...	MARK AS OVER ANNOTATED	Summary: IPI with MalT (P06993) from a large-scale interaction study. The observed physical interaction is a high-throughput binary-screen hit with no demonstrated client or regulatory consequence. Reason: Generic protein binding is uninformative, and a high-throughput interaction hit is insufficient to establish a functional DnaJ-MalT relationship for a promiscuous chaperone. Retain the source record for provenance but do not treat it as a supported molecular function without client-state or mechanistic evidence.
GO:0005515 protein binding	IPI PMID:15690043 Interaction network containing conserved and essential prote...	MODIFY	Summary: Separate IPI signature for DnaK (P0A6Y8) from the same interaction network study. Reason: Generic protein binding is uninformative for the established DnaJ-DnaK co-chaperone interaction. GO:0051087 specifically represents binding to the protein-folding chaperone DnaK. Proposed replacements: protein-folding chaperone binding
GO:0005515 protein binding	IPI PMID:18394994 Monitoring protein conformation along the pathway of chapero...	MODIFY	Summary: IPI with DnaK (P0A6Y8). Study monitoring protein conformation along the pathway of chaperonin-assisted folding. The DnaJ-DnaK interaction is well-established and is better represented by GO:0051087. Reason: "Protein binding" is uninformative. This DnaK interaction is a chaperone-cochaperone interaction better captured by GO:0051087 "protein-folding chaperone binding". Proposed replacements: protein-folding chaperone binding
GO:0005515 protein binding	IPI PMID:19439666 Solution conformation of wild-type E. coli Hsp70 (DnaK) chap...	MODIFY	Summary: IPI with DnaK (P0A6Y8). Solution conformation study of DnaK complexed with ADP and substrate. Another instance of the DnaJ-DnaK chaperone interaction. Reason: "Protein binding" is uninformative. DnaJ-DnaK interaction is a core chaperone- cochaperone relationship, better annotated as GO:0051087. Proposed replacements: protein-folding chaperone binding
GO:0005515 protein binding	IPI PMID:22065753 Heat shock protein 70 kDa chaperone/DnaJ cochaperone complex...	MODIFY	Summary: IPI with DnaK (P0A6Y8). Study of the dynamic interface between Hsp70/DnaJ cochaperone complex. Further evidence of the DnaJ-DnaK chaperone interaction. Reason: "Protein binding" is uninformative. The DnaJ-DnaK dynamic interface is a chaperone-cochaperone interaction, better captured by GO:0051087. Proposed replacements: protein-folding chaperone binding
GO:0005515 protein binding	IPI PMID:24561554 The binary protein-protein interaction landscape of Escheric...	MARK AS OVER ANNOTATED	Summary: IPI with MalT (P06993) from a large-scale binary protein-protein interaction study of E. coli. Similar to PMID:15690043, this is a high-throughput interaction dataset. Reason: This independent high-throughput screen repeats a generic binary-interaction signal but does not establish whether MalT is a DnaJ client or whether the contact has a physiological consequence. For a promiscuous chaperone, the screen hit alone does not justify retaining bare protein binding as a function.
GO:0006457 protein folding	IDA PMID:9103205 Crystal structure of the nucleotide exchange factor GrpE bou...	MARK AS OVER ANNOTATED	Summary: IDA annotation from CAFA. PMID:9103205 describes the crystal structure of GrpE bound to the DnaK ATPase domain. While this paper provides insight into the DnaK/GrpE nucleotide exchange mechanism relevant to the chaperone cycle, it does not directly assay DnaJ protein folding activity. However, protein folding is well-established for DnaJ from other sources (PMID:7559385). Reason: Protein folding is correct DnaJ biology, but this CAFA-assigned row is not supported by its cited paper; the cached abstract describes only a GrpE-DnaK structure and never mentions DnaJ. Other DnaJ-specific rows retain the process; they do not repair this row's provenance. Supporting Evidence: PMID:7559385 The DnaJ protein of Escherichia coli and the DnaJ-like proteins of eukaryotes are known as molecular chaperones and specific regulators of DnaK-like proteins and are involved in protein folding and renaturation after stress.
GO:0032991 protein-containing complex	IDA PMID:9103205 Crystal structure of the nucleotide exchange factor GrpE bou...	MARK AS OVER ANNOTATED	Summary: IDA from CAFA. PMID:9103205 describes the GrpE-DnaK complex structure. DnaJ forms part of the DnaK/DnaJ/GrpE chaperone complex. However, GO:0032991 "protein-containing complex" is extremely general and not very informative. Reason: DnaJ participates in transient DnaK-DnaJ-GrpE chaperone assemblies, but this extremely broad CAFA term is unsupported by PMID:9103205. The cached abstract reports a complex between a GrpE dimer and DnaK and does not include DnaJ. The biology may be sound in the wider cycle, but this row's provenance does not establish it.
GO:0051082 unfolded protein binding	IDA PMID:9103205 Crystal structure of the nucleotide exchange factor GrpE bou...	MARK AS OVER ANNOTATED	Summary: IDA from CAFA citing the GrpE-DnaK crystal structure paper. DnaJ does bind unfolded substrates, but PMID:9103205 does not directly demonstrate this. Regardless of the reference, GO:0051082 should be modified to GO:0044183 as part of the obsoletion project, since DnaJ binding to unfolded proteins is in the context of chaperone activity. Reason: GO:0051082 is obsolete, and this CAFA-assigned IDA is additionally unsupported by PMID:9103205, whose cached abstract describes GrpE bound to DnaK and does not mention DnaJ or an unfolded client. DnaJ's valid chaperone activity is captured by other evidence-backed rows.
GO:0051087 protein-folding chaperone binding	IPI PMID:9103205 Crystal structure of the nucleotide exchange factor GrpE bou...	MARK AS OVER ANNOTATED	Summary: IPI with DnaK (P0A6Y8) from CAFA. DnaJ binds the protein-folding chaperone DnaK. While PMID:9103205 is about the GrpE-DnaK structure, the DnaJ-DnaK interaction is well-established. This is an appropriate and informative MF annotation. Reason: The DnaJ-DnaK interaction is biologically well established elsewhere, but this CAFA IPI is miscited. PMID:9103205 assays GrpE bound to DnaK and does not report DnaJ. Multiple correctly cited DnaK IPI rows support GO:0051087, so the biological term is retained through those sources rather than this row. Supporting Evidence: PMID:9860950 Chaperones of the Hsp70 family bind to unfolded or partially folded polypeptides to facilitate many cellular processes. ATP hydrolysis and substrate binding, the two key molecular activities of this chaperone, are modulated by the cochaperone DnaJ.
GO:0065003 protein-containing complex assembly	IDA PMID:9103205 Crystal structure of the nucleotide exchange factor GrpE bou...	MARK AS OVER ANNOTATED	Summary: IDA from CAFA. DnaJ participates in the assembly of the DnaK/DnaJ/GrpE chaperone complex and also in the assembly/disassembly of replication initiation complexes. While somewhat general, DnaJ does facilitate complex assembly as part of its chaperone function. Reason: DnaJ participates in assembly and remodeling events during its chaperone cycle, but PMID:9103205 establishes assembly of a GrpE-DnaK complex, not a DnaJ-containing complex. The CAFA row therefore overstates what this source establishes without making the broader DnaJ biology false.
GO:0005829 cytosol	IDA PMID:6220698 Escherichia coli dnaJ- and dnaK-gene products: synthesis in ...	ACCEPT	Summary: IDA from EcoCyc. Zylicz et al. (1983) identified DnaJ in minicells. DnaJ is primarily a cytoplasmic/cytosolic protein. The cytosol annotation is appropriate and consistent with UniProt subcellular location. Reason: Experimentally supported localization. DnaJ is a soluble cytoplasmic protein. Supporting Evidence: PMID:6220698 Escherichia coli dnaJ- and dnaK-gene products have been identified in a system of minicells
GO:0043335 protein unfolding	IDA PMID:20953191 The kinetic parameters and energy cost of the Hsp70 chaperon...	ACCEPT	Summary: IDA from EcoCyc. Sharma et al. (2010) demonstrated that the Hsp70 (DnaK)-Hsp40 (DnaJ)-NEF (GrpE) system acts as a polypeptide unfoldase, converting stably misfolded proteins into intermediates that spontaneously refold to native state. DnaJ acts upstream of or within this process by delivering substrates to DnaK. Reason: The DnaK/DnaJ/GrpE system functions as an unfoldase to convert misfolded proteins into refoldable intermediates. DnaJ is essential to this process. Supported by direct experimental evidence from PMID:20953191. Supporting Evidence: PMID:20953191 one Hsp70 molecule consumed five ATPs to effectively unfold a single misfolded protein into an intermediate that, upon chaperone dissociation, spontaneously refolded to the native state
GO:0005515 protein binding	IPI PMID:18995833 Molecular basis for regulation of the heat shock transcripti...	MODIFY	Summary: IPI with sigma32 (P0AGB3). Rodriguez et al. (2008) identified two distinct binding sites in sigma32 for DnaK and DnaJ. DnaJ binding destabilizes a distant region of sigma32. This is a functionally important interaction for heat shock regulation. Better captured by GO:0016989 "sigma factor antagonist activity" which is already annotated. Reason: "Protein binding" is uninformative. The DnaJ-sigma32 interaction represents sigma factor antagonist activity (GO:0016989), already annotated from PMID:8599944. Alternatively, GO:0051087 "protein-folding chaperone binding" could apply if considering sigma32 as a chaperone substrate. Proposed replacements: sigma factor antagonist activity Supporting Evidence: PMID:18995833 Here we identified two distinct sites in sigma(32) as binding sites for DnaK and DnaJ. DnaJ binding destabilizes a distant region of sigma(32) in close spatial vicinity of the DnaK-binding site
GO:0015035 protein-disulfide reductase activity	IDA PMID:11732919 Zinc fingers and thiol-disulfide oxidoreductase activities o...	KEEP AS NON CORE	Summary: IDA from EcoCyc. Tang and Wang (2001) showed DnaJ possesses reductase and oxidase activity mediated by the -C183PHC186- motif in zinc center 2. The C-terminal fragment (Q181-R376) shows full enzymatic activity. This is a secondary function dependent on the zinc finger cysteines. Reason: Experimentally demonstrated (PMID:11732919) but represents a secondary, non-core function of DnaJ. The thiol-disulfide oxidoreductase activity is mediated by the zinc finger cysteines and is distinct from the primary co-chaperone function. The physiological significance in vivo remains unclear. Supporting Evidence: PMID:11732919 DnaJ shows reductase activity and oxidase activity but little, if any, isomerase activity. The reductase activity is reversibly inhibited by EDTA. Zn2 is important for the enzymatic activity, and only -C(183)PHC(186)- among the four motifs of -CXXC- functions as the active site of the enzyme. file:ECOLI/DnaJ/DnaJ-hypotheses/prediction-disulfide-isomerase/openscientist.md at most, an in-vitro-only over-annotation
GO:0005515 protein binding	IPI PMID:9860950 Interaction of the Hsp70 molecular chaperone, DnaK, with its...	MODIFY	Summary: IPI with DnaK (P0A6Y8). Suh et al. (1998) provided genetic and biochemical evidence that DnaJ binds to at least two sites on DnaK: under the ATPase domain and near the substrate-binding pocket. This is the foundational DnaK-DnaJ interaction paper. Better captured by GO:0051087. Reason: "Protein binding" is uninformative. This key paper characterizes the DnaJ-DnaK co-chaperone interaction. GO:0051087 "protein-folding chaperone binding" is the appropriate specific term. Proposed replacements: protein-folding chaperone binding Supporting Evidence: PMID:9860950 By using both genetic and biochemical approaches, we provide evidence that DnaJ binds to at least two sites on the Escherichia coli Hsp70 family member DnaK
GO:0016989 sigma factor antagonist activity	IDA PMID:8599944 A cycle of binding and release of the DnaK, DnaJ and GrpE ch...	ACCEPT	Summary: IDA from EcoCyc. Gamer et al. (1996) demonstrated that DnaK and DnaJ cooperatively inhibit sigma32 transcriptional activity. DnaJ binds free sigma32 with a Kd of 20 nM and mediates efficient binding of DnaK to sigma32. This is a well-established regulatory function of the DnaK/DnaJ system. Reason: Well-supported by direct experimental evidence. DnaJ binds sigma32 and cooperates with DnaK to inhibit its transcriptional activity. This is a specialized core regulatory output of DnaJ's co-chaperone mechanism on the native client sigma32, rather than an unrelated biochemical activity. Supporting Evidence: PMID:8599944 DnaJ and DnaK bind free, but not RNA polymerase-bound, sigma32 with dissociation constants of 20 nM and 5 muM respectively. PMID:8599944 DnaK and DnaJ cooperatively inhibit sigma32 activity in heat shock gene transcription and GrpE partially reverses this inhibition.
GO:0005515 protein binding	IPI PMID:1534276 Physical interaction between heat shock proteins DnaK, DnaJ,...	MODIFY	Summary: IPI with sigma32 (P0AGB3). Gamer et al. (1992) demonstrated physical interaction between DnaK, DnaJ, GrpE and sigma32 in vivo, with DnaJ-sigma32 association being distinct from DnaK-sigma32 interaction (resistant to ATP). This is better captured by the sigma factor antagonist activity annotation. Reason: "Protein binding" is uninformative. The DnaJ-sigma32 interaction represents a functionally characterized regulatory interaction. GO:0016989 "sigma factor antagonist activity" is already annotated for this function. Proposed replacements: sigma factor antagonist activity Supporting Evidence: PMID:1534276 an interaction of DnaJ with sigma 32 exists that is distinguishable from an interaction of DnaK and GrpE with sigma 32: addition of ATP disrupts the association of DnaK and GrpE with sigma 32, but not the association of DnaJ with sigma 32.
GO:0009408 response to heat	IMP PMID:2144273 Isolation and characterization of dnaJ null mutants of Esche...	ACCEPT	Summary: IMP from EcoCyc. Sell et al. (1990) showed that dnaJ null mutants did not grow well above 30C, formed progressively smaller colonies at higher temperatures, and could not grow at 43C. This demonstrates DnaJ is required for growth at elevated temperatures, directly supporting response to heat. Reason: Direct mutant phenotype evidence. DnaJ null mutants are heat-sensitive, demonstrating DnaJ is essential for the heat shock response above 42C. Supporting Evidence: PMID:2144273 dnaJ-insertion mutants did not grow as well as the wild type at temperatures above 30 degrees C, although they blocked lambda DNA replication at all temperatures. The dnaJ-insertion mutants formed progressively smaller colonies at higher temperatures, up to 42 degrees C, and did not form colonies at 43 degrees C.
GO:0016032 viral process	IDA PMID:1361234 Activity of the Hsp70 chaperone complex--DnaK, DnaJ, and Grp...	KEEP AS NON CORE	Summary: IDA from EcoCyc. Hoffmann et al. (1992) demonstrated that the DnaK/DnaJ/GrpE chaperone complex is required for initiating phage lambda DNA replication by sequestering and releasing lambda P protein from the preprimosomal complex. DnaJ forms an ATP-dependent ternary complex with DnaK and lambda P. Reason: DnaJ participates in phage lambda DNA replication as part of the chaperone system that releases lambda P protein. This is a well-established but non-core function representing the chaperone system being co-opted by phage. Supporting Evidence: PMID:1361234 We have discovered an ATP-dependent ternary interaction between P, DnaK, and DnaJ; this P.DnaK.DnaJ complex is dissociated by GrpE.
GO:0016032 viral process	IMP PMID:2144273 Isolation and characterization of dnaJ null mutants of Esche...	KEEP AS NON CORE	Summary: IMP from EcoCyc. Sell et al. (1990) showed that dnaJ null mutants blocked lambda phage growth at all temperatures. None of the suppressor mutations that restored bacterial growth also restored lambda phage propagation. Reason: DnaJ is required for phage lambda DNA replication. Mutant phenotype evidence is strong (PMID:2144273). Non-core because this is the phage co-opting the host chaperone system. Supporting Evidence: PMID:2144273 they blocked lambda DNA replication at all temperatures...None of these suppressor mutations restored the ability of the host to propagate phage lambda.
GO:0016032 viral process	IDA PMID:3889001 Purification and properties of the dnaJ replication protein ...	KEEP AS NON CORE	Summary: IDA from EcoCyc. Zylicz et al. (1985) purified DnaJ and showed it is required at a very early step in lambda DNA replication using an in vitro complementation assay. This is the original biochemical characterization of DnaJ function. Reason: Historical paper demonstrating DnaJ function in lambda DNA replication. Non-core as this is phage co-opting host chaperone function. Supporting Evidence: PMID:3889001 we have shown that the dnaJ protein is required at a very early step in the DNA replication process.
GO:0042803 protein homodimerization activity	IDA PMID:3889001 Purification and properties of the dnaJ replication protein ...	KEEP AS NON CORE	Summary: IDA from EcoCyc. Zylicz et al. (1985) determined that DnaJ has a native Mr of 76,000 under non-denaturing conditions versus 37,000 under denaturing conditions, indicating it exists as a homodimer. UniProt confirms DnaJ is a homodimer. Reason: The native molecular mass supports homodimerization, so the annotation is retained. Oligomeric state is structural context rather than a direct core chaperone or regulatory activity. Supporting Evidence: PMID:3889001 a basic (pI 8.5), yet hydrophobic, protein of Mr 37,000 and 76,000 under denaturing and native conditions, respectively
GO:0009408 response to heat	IEP PMID:8349564 Characterization of twenty-six new heat shock genes of Esche...	ACCEPT	Summary: IEP from EcoliWiki. Chuang and Blattner (1993) characterized heat shock genes including DnaJ, showing heat-induced expression kinetics similar to other major heat shock proteins (DnaK, GroEL, GroES). DnaJ expression is induced by heat shock. Reason: DnaJ is a well-known heat shock protein (HSP40) induced by heat stress. Expression evidence is consistent with IMP evidence from PMID:2144273 and UniProt annotation of heat-shock induction under HtpR control. Supporting Evidence: PMID:8349564 In vivo expression kinetics of seven of eight examined new proteins were found to be similar to those of the four most studied heat shock proteins, DnaK, DnaJ, GroEL (MopA), and GroES (MopB).
GO:0006260 DNA replication	IMP PMID:2144273 Isolation and characterization of dnaJ null mutants of Esche...	MODIFY	Summary: IMP from EcoliWiki. Sell et al. (1990) showed dnaJ null mutants blocked lambda DNA replication at all temperatures. DnaJ is required for the initiation of phage lambda DNA replication as part of the chaperone system. Reason: The experiment demonstrates a host chaperone requirement for bacteriophage lambda genome replication, not generic cellular DNA replication. GO:0044829 captures DnaJ promoting viral genome replication without implying a core host replisome function. Proposed replacements: host-mediated activation of viral genome replication Supporting Evidence: PMID:2144273 they blocked lambda DNA replication at all temperatures
GO:0008270 zinc ion binding	IDA PMID:8662861 Structure-function analysis of the zinc finger region of the...	ACCEPT	Summary: IDA from EcoliWiki. Banecki et al. (1996) demonstrated that two Zn(II) ions interact with each DnaJ monomer using quantitative zinc release assays and atomic absorption. The zinc finger region is important for DnaK-substrate complex stabilization. Reason: Direct experimental demonstration of zinc binding. DnaJ has two zinc centers with distinct functional roles (PMID:8662861, PMID:12941935). Supporting Evidence: PMID:8662861 Quantitation of the released Zn(II) ions, upon challenge with p-hydroxymercuriphenylsulfonic acid, and by atomic absorption showed that two Zn(II) ions interact with each monomer of DnaJ.
GO:0016020 membrane	IDA PMID:3889001 Purification and properties of the dnaJ replication protein ...	KEEP AS NON CORE	Summary: IDA from EcoliWiki. Zylicz et al. (1985) purified DnaJ from the membrane fraction of an overproducing strain. DnaJ is described as hydrophobic and membrane-associated. However, DnaJ is primarily a cytoplasmic/cytosolic protein. The membrane association may be due to DnaJ interacting with membrane-associated substrates or its hydrophobic Gly/Phe-rich region. Reason: DnaJ was purified from the membrane fraction and shown to have membrane affinity. UniProt lists subcellular location as Cytoplasm, but early studies consistently found membrane association (PMID:3889001, PMID:6220698). This likely represents a secondary localization or substrate interaction. Supporting Evidence: PMID:3889001 we purified the dnaJ protein to homogeneity from the membrane fraction of an overproducing strain of bacteria. The purified dnaJ protein was shown to be a basic (pI 8.5), yet hydrophobic, protein
GO:0008270 zinc ion binding	IDA PMID:11985624 Systematic search for zinc-binding proteins in Escherichia c...	ACCEPT	Summary: IDA from EcoliWiki. Katayama et al. (2002) performed a systematic search for zinc-binding proteins in E. coli using radioactive Zn(II) binding assays. DnaJ was identified as a known zinc-binding protein in this screen. Reason: Confirms DnaJ zinc binding by an independent experimental approach. Consistent with other IDA evidence for zinc ion binding (PMID:8662861).
GO:0005737 cytoplasm	IDA PMID:6220698 Escherichia coli dnaJ- and dnaK-gene products: synthesis in ...	ACCEPT	Summary: IDA from EcoliWiki. Zylicz et al. (1983) identified DnaJ in minicells and showed it has membrane affinity. The cytoplasm annotation is appropriate as DnaJ is primarily cytoplasmic. Consistent with IBA and IEA annotations. Reason: Direct experimental evidence. DnaJ identified in minicells as a cytoplasmic protein with membrane affinity (PMID:6220698). Supporting Evidence: PMID:6220698 Escherichia coli dnaJ- and dnaK-gene products have been identified in a system of minicells infected with the appropriate transducing lambda phages.
GO:0016020 membrane	IDA PMID:6220698 Escherichia coli dnaJ- and dnaK-gene products: synthesis in ...	KEEP AS NON CORE	Summary: IDA from EcoliWiki. Zylicz et al. (1983) showed both DnaJ and DnaK are membrane-bound using equilibrium sedimentation in metrizamide density gradients. Reason: Experimentally demonstrated membrane association. DnaJ shows membrane affinity, consistent with its hydrophobic character and membrane fraction purification (PMID:3889001). Supporting Evidence: PMID:6220698 Equilibrium sedimentation of minicell lysates in metrizamide density gradients has revealed that both these host proteins, indispensable for lambda DNA replication, are membrane-bound.
GO:0003756 protein disulfide isomerase activity	IDA PMID:7559385 A novel function of Escherichia coli chaperone DnaJ. Protein...	MODIFY	Summary: IDA from EcoliWiki. de Crouy-Chanel et al. (1995) showed DnaJ catalyzes protein disulfide formation, reduction, and isomerization (refolding of randomly oxidized RNase). However, Tang and Wang (2001, PMID:11732919) found that DnaJ shows reductase and oxidase activity but "little, if any, isomerase activity." The isomerase annotation may be an over-interpretation. Reason: While PMID:7559385 initially reported disulfide isomerase activity, the more detailed follow-up study (PMID:11732919) found DnaJ has "little, if any, isomerase activity" and primarily shows reductase and oxidase activities. GO:0015035 "protein-disulfide reductase activity" is already annotated and is the more accurate term. The isomerase activity claim was not confirmed. Proposed replacements: protein-disulfide reductase activity Supporting Evidence: PMID:11732919 DnaJ shows reductase activity and oxidase activity but little, if any, isomerase activity. PMID:7559385 DnaJ, like thioredoxin, protein-disulfide isomerase, and DsbA, possesses an active dithiol/disulfide group and catalyzes protein disulfide formation (oxidative renaturation of reduced RNase), reduction (reduction of insulin disulfides), and isomerization (refolding of randomly oxidized RNase).
GO:0006457 protein folding	IDA PMID:7559385 A novel function of Escherichia coli chaperone DnaJ. Protein...	ACCEPT	Summary: IDA from EcoliWiki. de Crouy-Chanel et al. (1995) demonstrated DnaJ involvement in protein folding and renaturation after stress. This is a core function. Reason: Core biological process for DnaJ. Well-supported experimental evidence. Supporting Evidence: PMID:7559385 The DnaJ protein of Escherichia coli and the DnaJ-like proteins of eukaryotes are known as molecular chaperones and specific regulators of DnaK-like proteins and are involved in protein folding and renaturation after stress.
GO:0008270 zinc ion binding	IMP PMID:12941935 The roles of the two zinc binding sites in DnaJ.	ACCEPT	Summary: IMP from EcoliWiki. Linke et al. (2003) showed that mutating zinc-coordinating cysteines to serine in either zinc center 1 (C144S/C147S/C197S/C200S) or zinc center 2 (C161S/C164S/C183S/C186S) had distinct functional effects, demonstrating the importance of zinc binding for DnaJ activity. Reason: Mutant phenotype evidence confirming the functional importance of zinc binding. Zinc center 1 is required for DnaK-independent chaperone activity, while zinc center 2 is essential for DnaK interaction and overall function. Supporting Evidence: PMID:12941935 in the absence of zinc center I, the autonomous, DnaK-independent chaperone activity of DnaJ is dramatically reduced...The DnaJ zinc center II, on the other hand, was found to be absolutely essential for the in vivo and in vitro function of DnaJ.
GO:0042026 protein refolding	IDA PMID:7559385 A novel function of Escherichia coli chaperone DnaJ. Protein...	ACCEPT	Summary: IDA from EcoliWiki. de Crouy-Chanel et al. (1995) demonstrated DnaJ involvement in protein renaturation (refolding) after stress, including refolding of randomly oxidized RNase. This is a core function of the DnaK/DnaJ/GrpE system. Reason: Core function. DnaJ participates in refolding of stress-denatured proteins as part of the DnaK/DnaJ/GrpE chaperone system. Experimentally demonstrated. Supporting Evidence: PMID:7559385 DnaJ-like proteins of eukaryotes are known as molecular chaperones and specific regulators of DnaK-like proteins and are involved in protein folding and renaturation after stress.
GO:0051082 unfolded protein binding	IDA PMID:7559385 A novel function of Escherichia coli chaperone DnaJ. Protein...	MODIFY	Summary: IDA from EcoliWiki. de Crouy-Chanel et al. (1995) showed DnaJ binds unfolded proteins as part of its chaperone function. However, GO:0051082 is now formally obsolete. DnaJ binding to unfolded substrates is part of the chaperone cycle, not an independent binding function. Reason: GO:0051082 is now formally obsolete. DnaJ binds unfolded proteins in the context of co-chaperone activity. GO:0044183 "protein folding chaperone" is the appropriate interim replacement, capturing the functional context of this binding. Proposed replacements: protein folding chaperone Supporting Evidence: PMID:7559385 DnaJ, like thioredoxin, protein-disulfide isomerase, and DsbA, possesses an active dithiol/disulfide group and catalyzes protein disulfide formation
GO:0001671 ATPase activator activity	EXP PMID:1826368 Escherichia coli DnaJ and GrpE heat shock proteins jointly s...	NEW	Summary: Proposed annotation for DnaJ's direct stimulation of DnaK ATP hydrolysis through its conserved J-domain HPD motif. Reason: PMID:1826368 shows that DnaJ alone accelerates hydrolysis of DnaK-bound ATP. GO:0001671 is the current specific molecular-function term for binding to and increasing an ATP hydrolysis activity and captures this defining co-chaperone mechanism. Supporting Evidence: PMID:1826368 The action of the DnaJ and GrpE proteins may be sequential, since the presence of DnaJ alone leads to an acceleration in the rate of hydrolysis of the DnaK-bound ATP.

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