DnaK

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0016887 ATP hydrolysis activity	IBA GO_REF:0000033	ACCEPT	Summary: DnaK has intrinsic ATPase activity that is central to its chaperone cycle. The ATP hydrolysis rate is stimulated by substrates and DnaJ (PMID:7776367). IBA annotation is well-supported phylogenetically across the HSP70 family and experimentally validated for DnaK. Reason: Core enzymatic activity of DnaK. ATP hydrolysis drives the conformational cycle essential for chaperone function. Well-documented experimentally (PMID:7776367, PMID:7937953). Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000452648 · PANTHER:PTN000452648 SUPPORTS TRANSFER Current PTHR19375 PAINT retains GO:0016887 at this ancestral node. FB:FBgn0001218 · FB:FBgn0001218 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. MGI:MGI:105384 · MGI:MGI:105384 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. PomBase:SPAC664.11 · PomBase:SPAC664.11 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. RGD:621725 · RGD:621725 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. SGD:S000000004 · SGD:S000000004 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. SGD:S000000171 · SGD:S000000171 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. SGD:S000002388 · SGD:S000002388 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. SGD:S000003571 · SGD:S000003571 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. SGD:S000003806 · SGD:S000003806 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. SGD:S000004361 · SGD:S000004361 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. SGD:S000005153 · SGD:S000005153 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. UniProtKB:P0A6Z1 · UniProtKB:P0A6Z1 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. UniProtKB:P0DMV8 · UniProtKB:P0DMV8 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. UniProtKB:P0DMV9 · UniProtKB:P0DMV9 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. UniProtKB:P11021 · UniProtKB:P11021 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. UniProtKB:P17066 · UniProtKB:P17066 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. UniProtKB:P38646 · UniProtKB:P38646 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. UniProtKB:P77319 · UniProtKB:P77319 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. UniProtKB:Q57VR7 · UniProtKB:Q57VR7 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. WB:WBGene00002005 · WB:WBGene00002005 SUPPORTS TRANSFER Listed descendant evidence for the current ATP-hydrolysis assertion. Supporting Evidence: PMID:7776367 DnaK ATPase was stimulated by substrates (ninefold) and DnaJ (13-fold) through stimulation of the rate limiting step, gamma-phosphate cleavage PMID:7937953 upon interaction with luciferase-DnaJ, DnaK hydrolyzes its bound ATP, resulting in the formation of a stable luciferase-DnaK-DnaJ complex
GO:0031072 heat shock protein binding	IBA GO_REF:0000033	ACCEPT	Summary: DnaK directly binds its co-chaperones DnaJ (Hsp40) and GrpE, as well as HtpG (Hsp90) and ClpB (Hsp100). The IBA annotation reflects conserved interactions across the HSP70 family. Multiple experimental studies confirm these interactions in E. coli (PMID:9103205, PMID:2522091, PMID:21525416). Reason: The current PAINT node placement is valid, and GO:0031072 preserves the experimentally supported heat-shock-partner interactions with HtpG and ClpB in addition to DnaJ and GrpE. The distinct GO:0051087 annotations are retained separately rather than used to collapse this sound IBA assertion. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000452648 · PANTHER:PTN000452648 SUPPORTS TRANSFER Current PTHR19375 PAINT retains GO:0031072 at this node, and the experimentally supported DnaK interactions are consistent with the transfer. RGD:1311806 · RGD:1311806 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. UniProtKB:P0DMV8 · UniProtKB:P0DMV8 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. UniProtKB:P0DMV9 · UniProtKB:P0DMV9 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. UniProtKB:P11142 · UniProtKB:P11142 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. UniProtKB:P17066 · UniProtKB:P17066 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. UniProtKB:P34931 · UniProtKB:P34931 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. UniProtKB:Q8IB24 · UniProtKB:Q8IB24 SUPPORTS TRANSFER Listed descendant evidence for the current node assertion. Supporting Evidence: PMID:9103205 Crystal structure of the nucleotide exchange factor GrpE bound to the ATPase domain of the molecular chaperone DnaK PMID:21525416 Results indicate that E. coli Hsp90 and DnaK interact in vivo and in vitro
GO:0044183 protein folding chaperone	IBA GO_REF:0000033	ACCEPT	Summary: DnaK is the canonical bacterial protein folding chaperone (foldase). It assists protein folding through iterative ATP-driven binding-and-release cycles (PMID:7937953). The IBA annotation is well-supported and represents a core function of the HSP70 family. Reason: Core molecular function of DnaK. The IBA captures the foldase activity at the correct level of specificity. DnaK has both GO:0044183 (general foldase) and GO:0140662 (ATP-dependent foldase) annotations; both are appropriate with GO:0140662 being more specific. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000452648 · PANTHER:PTN000452648 SUPPORTS TRANSFER Current PTHR19375 PAINT retains GO:0044183 at this ancestral node. FB:FBgn0266599 · FB:FBgn0266599 SUPPORTS TRANSFER Listed descendant evidence for the current foldase assertion. MGI:MGI:95835 · MGI:MGI:95835 SUPPORTS TRANSFER Listed descendant evidence for the current foldase assertion. MGI:MGI:96244 · MGI:MGI:96244 SUPPORTS TRANSFER Listed descendant evidence for the current foldase assertion. MGI:MGI:99517 · MGI:MGI:99517 SUPPORTS TRANSFER Listed descendant evidence for the current foldase assertion. UniProtKB:P0A6Y8 · DnaK SUPPORTS TRANSFER DnaK's own direct foldase evidence is valid descendant evidence, not circular propagation. UniProtKB:P0DMV8 · UniProtKB:P0DMV8 SUPPORTS TRANSFER Listed descendant evidence for the current foldase assertion. UniProtKB:P0DMV9 · UniProtKB:P0DMV9 SUPPORTS TRANSFER Listed descendant evidence for the current foldase assertion. Supporting Evidence: PMID:7937953 Several rounds of ATP-dependent interaction with DnaK and DnaJ are required for fully efficient folding file:ECOLI/DnaK/DnaK-deep-research-falcon.md DnaK is an ATP-dependent molecular chaperone
GO:0005829 cytosol	IBA GO_REF:0000033	ACCEPT	Summary: DnaK is predominantly a cytosolic protein. This is supported by multiple proteomic studies (PMID:15911532, PMID:18304323) and IBA phylogenetic inference. Reason: Well-established localization for DnaK, confirmed by both IDA and IBA evidence. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000751549 · PANTHER:PTN000751549 SUPPORTS TRANSFER Current PTHR19375 PAINT retains GO:0005829 at this ancestral node. UniProtKB:P0A6Y8 · DnaK SUPPORTS TRANSFER DnaK's direct cytosolic localization is valid descendant evidence, not circular propagation. UniProtKB:P0A6Z1 · UniProtKB:P0A6Z1 SUPPORTS TRANSFER Listed descendant evidence for the current cytosol assertion.
GO:0042026 protein refolding	IBA GO_REF:0000033	ACCEPT	Summary: DnaK is directly involved in refolding heat-damaged proteins. Schroder et al. (1993) showed that DnaK, DnaJ, and GrpE are essential for reactivation of heat-inactivated luciferase both in vivo and in vitro (PMID:7900997). Skowyra et al. (1990) demonstrated DnaK reactivates heat-inactivated RNA polymerase in an ATP-dependent manner (PMID:2203539). Reason: Core biological process for DnaK. Protein refolding (repair of heat-damaged proteins) is one of the best-characterized functions of the DnaK/DnaJ/GrpE system. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000452648 · PANTHER:PTN000452648 SUPPORTS TRANSFER Current PTHR19375 PAINT retains GO:0042026 at this ancestral node. SGD:S000000004 · SGD:S000000004 SUPPORTS TRANSFER Listed descendant evidence for the current refolding assertion. SGD:S000003806 · SGD:S000003806 SUPPORTS TRANSFER Listed descendant evidence for the current refolding assertion. UniProtKB:P0DMV8 · UniProtKB:P0DMV8 SUPPORTS TRANSFER Listed descendant evidence for the current refolding assertion. UniProtKB:P0DMV9 · UniProtKB:P0DMV9 SUPPORTS TRANSFER Listed descendant evidence for the current refolding assertion. UniProtKB:P11142 · UniProtKB:P11142 SUPPORTS TRANSFER Listed descendant evidence for the current refolding assertion. UniProtKB:P17066 · UniProtKB:P17066 SUPPORTS TRANSFER Listed descendant evidence for the current refolding assertion. UniProtKB:P34931 · UniProtKB:P34931 SUPPORTS TRANSFER Listed descendant evidence for the current refolding assertion. UniProtKB:P54652 · UniProtKB:P54652 SUPPORTS TRANSFER Listed descendant evidence for the current refolding assertion. Supporting Evidence: PMID:7900997 DnaK, DnaJ and GrpE did not prevent luciferase inactivation, but were essential for its reactivation PMID:2203539 heat-inactivated and aggregated RNA polymerase is both disaggregated and reactivated following simultaneous incubation with DnaK protein and hydrolyzable ATP
GO:0045892 negative regulation of DNA-templated transcription	IEA GO_REF:0000108	ACCEPT	Summary: This IEA annotation is inferred from GO:0016989 (sigma factor antagonist activity) via logical inference. DnaK binds and inactivates sigma32, which represses heat shock gene transcription (PMID:8599944). The inference is sound since antagonizing sigma32 leads to negative regulation of sigma32-dependent transcription. Reason: Logically sound inference from the experimentally validated sigma factor antagonist activity (GO:0016989). DnaK-mediated sequestration of sigma32 represses heat shock gene transcription. Supporting Evidence: PMID:8599944 DnaK and DnaJ cooperatively inhibit sigma32 activity in heat shock gene transcription
GO:0000166 nucleotide binding	IEA GO_REF:0000043	ACCEPT	Summary: IEA annotation from UniProt keyword mapping. DnaK binds both ATP and ADP, which is well-established experimentally (PMID:7776367, PMID:19439666). This is a broader parent of the more specific ATP binding annotation. Reason: Correct but very general. Subsumed by more specific ATP binding (GO:0005524) and ADP binding (GO:0043531) annotations which are experimentally validated. Acceptable as an IEA annotation.
GO:0005524 ATP binding	IEA GO_REF:0000120	ACCEPT	Summary: IEA annotation for ATP binding, which is also supported by direct IDA evidence (PMID:9103205, PMID:7776367). DnaK has a well-characterized N-terminal ATPase domain. Reason: Correct annotation. ATP binding is a core feature of DnaK's N-terminal nucleotide-binding domain. Redundant with IDA-supported annotations but acceptable.
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: IEA annotation from UniProt subcellular location mapping. DnaK is predominantly cytoplasmic, confirmed by HDA (PMID:16858726) and IDA (PMID:15911532, PMID:18304323) evidence as well. Reason: Correct localization. Broader than cytosol (GO:0005829) but acceptable as IEA.
GO:0005886 plasma membrane	IEA GO_REF:0000044	KEEP AS NON CORE	Summary: IEA annotation from UniProt subcellular location. UniProt lists DnaK as a peripheral inner membrane protein (PMID:16079137). DnaK has also been found associated with membrane fractions (PMID:16858726 HDA). This is a secondary localization. Reason: DnaK is primarily cytosolic but has been detected at the cell inner membrane as a peripheral protein. This is not a core localization but is supported by UniProt annotations citing PMID:16079137.
GO:0006260 DNA replication	IEA GO_REF:0000043	KEEP AS NON CORE	Summary: IEA annotation from UniProt keyword mapping (KW-0235 DNA replication). UniProt describes DnaK as essential for phage lambda DNA replication and involved in chromosomal DNA replication through interaction with DnaA. This reflects a genuine but non-core function. Reason: DnaK's role in DNA replication is well-documented for phage lambda (releasing lambda O and P from the preprimosomal complex) and proposed for chromosomal replication via DnaA interaction. However, this is not DnaK's primary evolved function -- it reflects chaperone activity applied to replication machinery, not a direct replication function.
GO:0006457 protein folding	IEA GO_REF:0000002	ACCEPT	Summary: IEA annotation from InterPro (IPR012725, Chaperone_DnaK). DnaK is a core protein folding chaperone. This BP annotation is correct and also supported by IDA evidence (PMID:9103205). Reason: Protein folding is the core biological process in which DnaK participates. This IEA is consistent with the extensive experimental evidence.
GO:0016887 ATP hydrolysis activity	IEA GO_REF:0000002	ACCEPT	Summary: IEA annotation from InterPro (IPR013126, Hsp_70_fam). Duplicates the IBA annotation for the same term. DnaK has well-characterized intrinsic ATPase activity. Reason: Correct. Duplicate of the IBA annotation but from a different evidence source. ATP hydrolysis is central to DnaK function.
GO:0051082 unfolded protein binding	IEA GO_REF:0000002	MODIFY	Summary: IEA annotation from InterPro (IPR012725). GO:0051082 is now formally obsolete (go-ontology#30962). DnaK does bind unfolded proteins, but this binding is in the context of its foldase activity, not as a passive binder. The function is better captured by GO:0044183 (protein folding chaperone) or GO:0140662 (ATP-dependent protein folding chaperone), both of which DnaK already has. Reason: GO:0051082 is now formally obsolete. DnaK's binding of unfolded proteins is mechanistically part of its ATP-dependent foldase cycle, not passive binding. The correct MF is GO:0044183 or its child GO:0140662. DnaK can also function as a holdase in some contexts (PMID:2203539, ATP-independent protection from aggregation), but the holdase NTR has not yet been created. Proposed replacements: protein folding chaperone Supporting Evidence: PMID:7937953 DnaK, the Hsp70 protein of Escherichia coli, is regulated by the chaperone protein DnaJ and the cofactor GrpE...we have analyzed a model reaction in which DnaK, DnaJ, and GrpE mediate the folding of denatured firefly luciferase
GO:0051087 protein-folding chaperone binding	IEA GO_REF:0000117	ACCEPT	Summary: IEA annotation from ARBA machine learning. DnaK binds multiple chaperones including DnaJ, GrpE, HtpG, and ClpB. This is also supported by IPI evidence (PMID:9103205, PMID:21525416). Reason: Correct. DnaK physically interacts with multiple protein-folding chaperones as part of its functional cycle.
GO:0005515 protein binding	IPI PMID:10521435 Structural features required for the interaction of the Hsp7...	MODIFY	Summary: IPI with DnaJ (P08622). Suh et al. (1999) characterized structural features required for DnaK-DnaJ interaction. This is a functionally meaningful chaperone-co-chaperone interaction central to DnaK function. Reason: The DnaK-DnaJ interaction is a core co-chaperone interaction, not generic protein binding. Better captured by GO:0031072 (heat shock protein binding) or GO:0051087 (protein-folding chaperone binding), which DnaK already has. Proposed replacements: protein-folding chaperone binding
GO:0005515 protein binding	IPI PMID:15690043 Interaction network containing conserved and essential prote...	KEEP AS NON CORE	Summary: IPI from a large-scale interaction study (Butland et al. 2005) detecting DnaK interactions with multiple E. coli proteins including DnaJ (P08622), GrpE (P09372), RpoH (P0AGB3), and many others. As a chaperone, DnaK is expected to interact with a wide range of cellular proteins. GO:0005515 is uninformative. Reason: The IPI set asserts observed physical interactions and there is no contradictory evidence. Because the partners are heterogeneous, no single specific replacement fits the entire grouped signature; generic binding is retained as non-core.
GO:0005515 protein binding	IPI PMID:16139413 Analysis of the Escherichia coli RNA degradosome composition...	KEEP AS NON CORE	Summary: IPI with Rne/RNase E (P21513). DnaK was found associated with the RNA degradosome complex. This likely reflects a chaperone-substrate interaction rather than a stable functional complex. Reason: The IPI supports an observed DnaK-RNase E association and there is no contradictory evidence. Its mechanistic meaning is unclear, so the generic interaction is retained as non-core rather than treated as invalid.
GO:0005515 protein binding	IPI PMID:16606699 Large-scale identification of protein-protein interaction of...	KEEP AS NON CORE	Summary: IPI from large-scale protein-protein interaction study (Arifuzzaman et al. 2006). DnaK interactions with GrpE, HtpG, RpoH, CbpA and others detected. Reason: These IPI partners are heterogeneous and the observed interactions are not contradicted. No one mechanistic replacement applies to the grouped row, so generic binding is retained as non-core.
GO:0005515 protein binding	IPI PMID:16858726 A complexomic study of Escherichia coli using two-dimensiona...	MODIFY	Summary: IPI from complexomic study (Lasserre et al. 2006) detecting DnaK interactions with GrpE (P09372) and ClpB (P63284) by 2D blue native/SDS-PAGE. Reason: Both GrpE and ClpB are protein-folding chaperone-system partners; the specific GO:0051087 term is more informative than generic protein binding. Proposed replacements: protein-folding chaperone binding
GO:0005515 protein binding	IPI PMID:17357109 70-kDa heat shock proteins: specific interactions with HLA-D...	KEEP AS NON CORE	Summary: IPI with human HLA-DR molecules (P04233, A0A0G4PYZ0). This is a cross-species (xenologous) interaction where E. coli DnaK binds human MHC class II molecules. This is an in vitro finding relevant to immunology but not to DnaK's native cellular function. Reason: Xenologous interaction with human HLA-DR. While demonstrating peptide-binding capacity of DnaK, this does not represent a native E. coli function.
GO:0005515 protein binding	IPI PMID:17968012 Analysis of sigma32 mutants defective in chaperone-mediated ...	KEEP AS NON CORE	Summary: IPI with RpoH/sigma32 (P0AGB3). Yura et al. (2007) analyzed sigma32 mutants defective in chaperone-mediated feedback control. DnaK binding to sigma32 is a central regulatory mechanism of the heat shock response. Reason: The IPI establishes a functionally important DnaK-sigma32 interaction, but physical-interaction evidence alone does not assert sigma factor antagonist activity. That activity is retained independently on the direct IDA annotation; this generic binding row is kept as non-core without overstating its evidence.
GO:0005515 protein binding	IPI PMID:18394994 Monitoring protein conformation along the pathway of chapero...	MODIFY	Summary: IPI with DnaJ (P08622). Sharma et al. (2008) studied chaperonin-assisted folding and DnaK-DnaJ cooperation. Functionally meaningful co-chaperone interaction. Reason: The DnaK-DnaJ co-chaperone interaction is specifically represented by GO:0051087; generic protein binding is uninformative. 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 DnaJ (P08622). Bertelsen et al. (2009) determined the solution structure of full-length DnaK complexed with ADP and substrate peptide. Important structural study showing domain dynamics. Reason: The IPI asserts the DnaK-DnaJ co-chaperone interaction, which is more specifically represented by GO:0051087. Proposed replacements: protein-folding chaperone binding
GO:0005515 protein binding	IPI PMID:19698713 DnaK-mediated association of ClpB to protein aggregates. A b...	MODIFY	Summary: IPI with ClpB (P63284). Acebrón et al. (2009) showed DnaK mediates association of ClpB to protein aggregates, forming a bichaperone network at aggregate surfaces. This is a functionally important disaggregation-related interaction. Reason: DnaK-ClpB interaction is a functionally meaningful chaperone-chaperone interaction for protein disaggregation, better captured by GO:0031072 (heat shock protein binding). Proposed replacements: heat shock protein binding
GO:0005515 protein binding	IPI PMID:21474779 Species-specific collaboration of heat shock proteins (Hsp) ...	MODIFY	Summary: IPI with ClpB (P63284). Miot et al. (2011) studied species-specific collaboration of Hsp70 and Hsp100 in thermotolerance and protein disaggregation. Reason: The DnaK-ClpB interaction is a chaperone-system interaction in protein disaggregation and is more specifically captured by GO:0031072. Proposed replacements: heat shock protein binding
GO:0005515 protein binding	IPI PMID:22065753 Heat shock protein 70 kDa chaperone/DnaJ cochaperone complex...	MODIFY	Summary: IPI with DnaJ (P08622). Ahmad et al. (2011) characterized the dynamic interface of the Hsp70/DnaJ cochaperone complex. Important structural study of co-chaperone interaction. Reason: The characterized DnaK-DnaJ dynamic interface is specifically represented by GO:0051087 rather than generic protein binding. Proposed replacements: protein-folding chaperone binding
GO:0005515 protein binding	IPI PMID:23160352 Hsp70 proteins bind Hsp100 regulatory M domains to activate ...	MODIFY	Summary: IPI with ClpB (P63284). Seyffer et al. (2012) showed that Hsp70 (DnaK) proteins bind to Hsp100 regulatory M domains to activate AAA+ disaggregase activity at aggregate surfaces. Reason: Functionally important DnaK-ClpB interaction for disaggregation activation. Better captured by GO:0031072 (heat shock protein binding). Proposed replacements: heat shock protein binding
GO:0005515 protein binding	IPI PMID:24561554 The binary protein-protein interaction landscape of Escheric...	MODIFY	Summary: IPI from binary protein-protein interaction landscape study (Rajagopala et al. 2014). Large-scale Y2H screen detecting DnaK interactions with HtpG (P0A6Z3) and CbpA (P36659). Reason: Both HtpG and CbpA are chaperone-system partners, so GO:0051087 is an evidence-matched specific replacement for the grouped IPI signature. Proposed replacements: protein-folding chaperone binding
GO:0005515 protein binding	IPI PMID:26545493 GroEL to DnaK chaperone network behind the stability modulat...	KEEP AS NON CORE	Summary: IPI with RpoH/sigma32 (P0AGB3). Patra et al. (2015) studied the GroEL-to-DnaK chaperone network behind sigma32 stability modulation. The DnaK-sigma32 interaction is a key regulatory mechanism. Reason: The IPI supports a DnaK-sigma32 interaction in the chaperone network that modulates sigma32 stability, but it does not by itself establish sigma factor antagonist activity. The generic binding row is retained as non-core; antagonist activity remains independently supported by direct IDA evidence.
GO:0005515 protein binding	IPI PMID:9103205 Crystal structure of the nucleotide exchange factor GrpE bou...	MODIFY	Summary: IPI with GrpE (P09372) from the crystal structure study of GrpE bound to the DnaK ATPase domain (Harrison et al. 1997). A dimer of GrpE binds asymmetrically to a single DnaK molecule. Reason: DnaK-GrpE is a core co-chaperone interaction essential for the DnaK functional cycle. Better captured by GO:0051087 (protein-folding chaperone binding). Proposed replacements: protein-folding chaperone binding Supporting Evidence: PMID:9103205 A dimer of GrpE binds asymmetrically to a single molecule of DnaK
GO:0009408 response to heat	IDA PMID:7023474 Positive regulatory gene for temperature-controlled proteins...	ACCEPT	Summary: Neidhardt and VanBogelen (1981) identified DnaK as a positive regulatory gene for temperature-controlled proteins. DnaK is one of the most highly induced heat shock proteins in E. coli. Reason: DnaK (Hsp70) is a major heat shock protein that is strongly induced upon heat stress. Response to heat is a core biological process for this gene.
GO:0009408 response to heat	IDA PMID:7900997 DnaK, DnaJ and GrpE form a cellular chaperone machinery capa...	ACCEPT	Summary: Schroder et al. (1993) demonstrated that DnaK, DnaJ, and GrpE form a chaperone machinery capable of repairing heat-induced protein damage. DnaK is essential for reactivation of heat-inactivated luciferase. Reason: Direct demonstration of DnaK function in the heat stress response, specifically repairing heat-damaged proteins. Supporting Evidence: PMID:7900997 DnaK, DnaJ and GrpE did not prevent luciferase inactivation, but were essential for its reactivation
GO:0009408 response to heat	IEP PMID:8349564 Characterization of twenty-six new heat shock genes of Esche...	ACCEPT	Summary: Chuang and Blattner (1993) characterized heat shock genes in E. coli and showed DnaK has expression kinetics typical of major heat shock proteins. IEP (expression pattern) evidence. Reason: DnaK is among the most well-characterized heat shock proteins. Its heat-induced expression pattern is consistent with its role in heat stress response. 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:0034620 cellular response to unfolded protein	IDA PMID:2203539 The E. coli dnaK gene product, the hsp70 homolog, can reacti...	ACCEPT	Summary: Skowyra et al. (1990) showed DnaK protects RNA polymerase from heat inactivation and reactivates heat-inactivated/aggregated RNA polymerase. This demonstrates DnaK's role in cellular response to unfolded proteins. Reason: DnaK is a central effector of the cellular response to unfolded proteins, both preventing aggregation and reactivating misfolded/aggregated proteins. Supporting Evidence: PMID:2203539 the dnaK gene product, protects the host RNA polymerase enzyme from heat inactivation in an ATP-independent reaction...heat-inactivated and aggregated RNA polymerase is both disaggregated and reactivated following simultaneous incubation with DnaK protein and hydrolyzable ATP
GO:0034620 cellular response to unfolded protein	IDA PMID:7900997 DnaK, DnaJ and GrpE form a cellular chaperone machinery capa...	ACCEPT	Summary: Schroder et al. (1993) showed DnaK/DnaJ/GrpE repair heat-damaged proteins. DnaJ associates with denatured luciferase, targets DnaK to the substrate, and together they prevent aggregation and enable reactivation. Reason: DnaK is essential for the cellular response to unfolded/denatured proteins. Supporting Evidence: PMID:7900997 DnaJ associated with denatured luciferase, targeted DnaK to the substrate and co-operated with DnaK to prevent luciferase aggregation at 42 degrees C
GO:0043335 protein unfolding	IDA PMID:20953191 The kinetic parameters and energy cost of the Hsp70 chaperon...	ACCEPT	Summary: Sharma et al. (2010) characterized DnaK as a polypeptide unfoldase, showing that Hsp70 consumes ATP to unfold a stably misfolded protein into an intermediate that spontaneously refolds to the native state. One DnaK consumed five ATPs to unfold one misfolded protein. Reason: DnaK's unfoldase activity is a key mechanistic feature of its chaperone function. By unfolding stably misfolded species, DnaK gives them another chance to fold correctly. This is a genuine and important aspect of DnaK function. 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:0140662 ATP-dependent protein folding chaperone	IDA PMID:2203539 The E. coli dnaK gene product, the hsp70 homolog, can reacti...	ACCEPT	Summary: Skowyra et al. (1990) showed DnaK reactivates heat-inactivated RNA polymerase in an ATP hydrolysis-dependent manner. This directly demonstrates ATP-dependent protein folding chaperone activity. Reason: Core molecular function of DnaK. GO:0140662 is the most specific and accurate MF term for DnaK -- it is a child of GO:0044183 (protein folding chaperone) combined with ATP dependence, exactly matching DnaK's mechanism. Supporting Evidence: PMID:2203539 heat-inactivated and aggregated RNA polymerase is both disaggregated and reactivated following simultaneous incubation with DnaK protein and hydrolyzable ATP
GO:0140662 ATP-dependent protein folding chaperone	IDA PMID:7937953 The ATP hydrolysis-dependent reaction cycle of the Escherich...	ACCEPT	Summary: Szabo et al. (1994) defined the complete ATP hydrolysis-dependent reaction cycle of the DnaK/DnaJ/GrpE system mediating folding of denatured luciferase. They showed multiple rounds of ATP-dependent binding and release are required for efficient folding. Reason: Definitive demonstration of DnaK's ATP-dependent chaperone cycle. This paper established the mechanistic framework for the DnaK system. Supporting Evidence: PMID:7937953 A single cycle of binding and release leads to folding of only a fraction of luciferase molecules. Several rounds of ATP-dependent interaction with DnaK and DnaJ are required for fully efficient folding
GO:1990169 stress response to copper ion	IMP PMID:35289645 Copper Induces Protein Aggregation, a Toxic Process Compensa...	KEEP AS NON CORE	Summary: Zuily et al. (2022) showed copper induces protein aggregation in E. coli and that molecular chaperones including DnaK compensate for this toxicity. IMP evidence indicates DnaK mutant phenotype is relevant to copper stress. Reason: Copper-induced protein aggregation triggers the chaperone response, with DnaK playing a compensatory role. This is a genuine but secondary function -- DnaK's chaperone activity is recruited to handle copper-induced misfolding, rather than copper stress response being an evolved function per se.
GO:0051087 protein-folding chaperone binding	IPI PMID:21525416 Heat shock protein 90 from Escherichia coli collaborates wit...	ACCEPT	Summary: Genest et al. (2011) showed E. coli Hsp90 (HtpG, P0A6Z3) collaborates with the DnaK chaperone system in client protein remodeling. DnaK and HtpG interact in vivo and in vitro. Reason: DnaK-HtpG (Hsp90) interaction is a functionally relevant chaperone-chaperone binding event important for client remodeling. GO:0051087 appropriately captures this. Supporting Evidence: PMID:21525416 Results indicate that E. coli Hsp90 and DnaK interact in vivo and in vitro, providing additional evidence to suggest that E. coli Hsp90 and the DnaK system function together
GO:0005515 protein binding	IPI PMID:30442809 Protein assemblies ejected directly from native membranes yi...	KEEP AS NON CORE	Summary: IPI with OmpA (P0A910) from native membrane mass spectrometry study (Chorev et al. 2018). DnaK was found associated with membrane protein complexes. Reason: The IPI supports an observed DnaK-OmpA association and there is no contradictory evidence. Its mechanistic interpretation is unresolved, so generic binding is retained as non-core.
GO:0005524 ATP binding	IDA PMID:9103205 Crystal structure of the nucleotide exchange factor GrpE bou...	ACCEPT	Summary: Harrison et al. (1997) solved the crystal structure of GrpE bound to the nucleotide-free ATPase domain of DnaK, which also provided structural context for ATP binding. The CAFA annotation cites this as IDA evidence for ATP binding. Reason: ATP binding is a core function of DnaK's N-terminal nucleotide-binding domain (NBD). Well-supported by structural and biochemical data. Supporting Evidence: PMID:9103205 The structure of the nucleotide-free ATPase domain in complex with GrpE resembles closely that of the nucleotide-bound mammalian Hsp70 homolog
GO:0006457 protein folding	IDA PMID:9103205 Crystal structure of the nucleotide exchange factor GrpE bou...	ACCEPT	Summary: CAFA annotation citing the GrpE-DnaK crystal structure paper. While this paper primarily addresses structure, the DnaK system's role in protein folding is implicit in the functional context of the chaperone cycle. Reason: Protein folding is the core biological process of DnaK. The abstract-only cache is primarily structural, but it identifies DnaK as a molecular chaperone and describes GrpE-mediated peptide release; the experimental curator had access to the full paper, so incomplete cached evidence is not grounds to overrule the IDA annotation.
GO:0032991 protein-containing complex	IDA PMID:9103205 Crystal structure of the nucleotide exchange factor GrpE bou...	KEEP AS NON CORE	Summary: Harrison et al. (1997) solved the crystal structure of the GrpE dimer bound to DnaK, demonstrating a stable protein-containing complex. DnaK forms functional complexes with its co-chaperones. Reason: The crystallized DnaK-GrpE assembly makes the statement factually sound, but GO:0032991 is a root-level cellular-component term that does not identify the functional chaperone assembly. It is therefore retained as a true but uninformative non-core localization rather than promoted as a core function. Supporting Evidence: PMID:9103205 A dimer of GrpE binds asymmetrically to a single molecule of DnaK
GO:0051082 unfolded protein binding	IDA PMID:9103205 Crystal structure of the nucleotide exchange factor GrpE bou...	MODIFY	Summary: CAFA annotation. The GrpE-DnaK crystal structure paper does describe DnaK's substrate- binding domain and its interaction with peptide substrates. However, GO:0051082 is now formally obsolete, and DnaK's function is better described as ATP-dependent protein folding chaperone (GO:0140662). Reason: GO:0051082 is now formally obsolete (go-ontology#30962). DnaK's substrate binding is mechanistically part of its foldase cycle. The appropriate replacement is GO:0044183 (protein folding chaperone) or GO:0140662 (ATP-dependent protein folding chaperone), both of which DnaK already has. Proposed replacements: ATP-dependent protein folding chaperone
GO:0051087 protein-folding chaperone binding	IPI PMID:9103205 Crystal structure of the nucleotide exchange factor GrpE bou...	ACCEPT	Summary: The IPI records DnaJ (P08622) as the interacting partner. DnaK-DnaJ binding is a core, repeatedly demonstrated co-chaperone interaction, although the abstract-only cache for this citation focuses on the GrpE-DnaK structure. Reason: Protein-folding chaperone binding is a core DnaK function and the exact GOA WITH/FROM identifies DnaJ. Because only the abstract is cached, its focus on GrpE is not grounds to overrule an experimental curator who had access to the full paper; independently cited DnaK-DnaJ IPI rows further support the biology.
GO:0065003 protein-containing complex assembly	IDA PMID:9103205 Crystal structure of the nucleotide exchange factor GrpE bou...	KEEP AS NON CORE	Summary: CAFA annotation citing the GrpE-DnaK crystal structure. The complex assembly (DnaK with GrpE dimer) was demonstrated crystallographically. However, this is a byproduct of DnaK's chaperone cycle rather than a primary function. Reason: DnaK does assemble into complexes with its co-chaperones (GrpE dimer, DnaJ), but complex assembly is not DnaK's primary function -- it is part of the chaperone mechanism. This is non-core.
GO:0016234 inclusion body	IDA PMID:15866952 Localization of chaperones DnaK and GroEL in bacterial inclu...	ACCEPT	Summary: Carrio and Villaverde (2005) showed by immunostaining and electron microscopy that DnaK localizes to the solvent-exposed surface of bacterial inclusion bodies. This represents DnaK's quality control function at sites of protein aggregation. Reason: DnaK localization to inclusion body surfaces is consistent with its role in protein quality control. It is recruited to aggregates where it acts to resolubilize and refold misfolded proteins. Supporting Evidence: PMID:15866952 chaperones DnaK and GroEL have been identified at the solvent-exposed surface of bacterial inclusion bodies and entrapped within these aggregates, respectively
GO:0005515 protein binding	IPI PMID:2522091 Escherichia coli DnaK and GrpE heat shock proteins interact ...	MODIFY	Summary: Johnson et al. (1989) demonstrated DnaK and GrpE interact both in vivo and in vitro by coimmunoprecipitation. This was one of the earliest demonstrations of the DnaK-GrpE functional interaction. Reason: DnaK-GrpE interaction is a core co-chaperone interaction better captured by GO:0051087 (protein-folding chaperone binding) rather than generic protein binding. Proposed replacements: protein-folding chaperone binding Supporting Evidence: PMID:2522091 Coimmunoprecipitation of DnaK+ and GrpE+ proteins from cell lysates with anti-DnaK antibodies demonstrated their interaction in vitro
GO:0016989 sigma factor antagonist activity	IDA PMID:8599944 A cycle of binding and release of the DnaK, DnaJ and GrpE ch...	ACCEPT	Summary: Gamer et al. (1996) showed DnaK and DnaJ cooperatively bind free sigma32 and inhibit its transcriptional activity in a cycle of binding and release regulated by GrpE and ATP. This constitutes sigma factor antagonist activity. Reason: DnaK directly inhibits sigma32 activity by binding it and preventing its association with RNA polymerase. This is an important regulatory function and represents a core, well-characterized regulatory MF of DnaK. The chaperone-mediated feedback control of the heat shock response depends on this activity. Supporting Evidence: PMID:8599944 DnaK and DnaJ cooperatively inhibit sigma32 activity in heat shock gene transcription and GrpE partially reverses this inhibition
GO:0005829 cytosol	IDA PMID:15911532 Localization, annotation, and comparison of the Escherichia ...	ACCEPT	Summary: IDA localization study (Lopez-Campistrous et al. 2005) confirming DnaK is present in the E. coli cytosol under different growth conditions. Reason: Cytosol is the primary localization of DnaK, confirmed by multiple independent studies.
GO:0005829 cytosol	IDA PMID:18304323 Protein abundance profiling of the Escherichia coli cytosol.	ACCEPT	Summary: IDA from protein abundance profiling of the E. coli cytosol (Ishihama et al. 2008). DnaK is one of the most abundant cytosolic proteins. Reason: Confirms cytosolic localization. DnaK is one of the most abundant proteins in the E. coli cytosol. Supporting Evidence: PMID:18304323 we identified 1103 proteins from the cytosolic fraction of the Escherichia coli strain MC4100. A measure of abundance is presented for each of the identified proteins
GO:0044183 protein folding chaperone	IDA PMID:10380927 Polypeptide flux through bacterial Hsp70: DnaK cooperates wi...	ACCEPT	Summary: Teter et al. (1999) showed DnaK transiently associates with a wide variety of nascent and newly synthesized polypeptides under nonstress conditions, demonstrating its role as a de novo protein folding chaperone. Combined deletion of trigger factor and DnaK is lethal. Reason: Definitive demonstration of DnaK as a de novo protein folding chaperone for nascent polypeptides. This is a core molecular function. Supporting Evidence: PMID:10380927 DnaK transiently associates with a wide variety of nascent and newly synthesized polypeptides, with a preference for chains larger than 30 kDa...Combined deletion of the trigger factor and DnaK genes is lethal under normal growth conditions
GO:0005524 ATP binding	IDA PMID:7776367 The role of ATP in the functional cycle of the DnaK chaperon...	ACCEPT	Summary: McCarty et al. (1995) characterized the ATP hydrolysis cycle of DnaK, showing that ATP-bound DnaK is the primary form initiating substrate interaction. Reason: Core function. ATP binding to DnaK's NBD drives its conformational cycle. This paper provided detailed kinetic characterization of the nucleotide cycle. Supporting Evidence: PMID:7776367 The rapid binding kinetics lead to the conclusion that ATP-bound DnaK is the primary form initiating interaction with substrates for chaperone activity
GO:0043531 ADP binding	IDA PMID:19439666 Solution conformation of wild-type E. coli Hsp70 (DnaK) chap...	ACCEPT	Summary: Bertelsen et al. (2009) determined the solution conformation of wild-type DnaK complexed with ADP and substrate peptide. ADP binding stabilizes the closed-lid conformation of the substrate-binding domain. Reason: ADP binding is an integral part of the DnaK chaperone cycle. In the ADP-bound state, DnaK has high affinity for substrate with slow exchange rates. Supporting Evidence: PMID:19439666 an experimental structure for wild-type, full-length DnaK, complexed with the peptide NRLLLTG and with ADP
GO:0043531 ADP binding	IDA PMID:7776367 The role of ATP in the functional cycle of the DnaK chaperon...	ACCEPT	Summary: McCarty et al. (1995) characterized DnaK's nucleotide binding properties, including ADP binding and its role in the functional cycle. Reason: ADP binding is essential for the DnaK chaperone cycle. GrpE stimulates ADP release, which is a key regulatory step.
GO:0051082 unfolded protein binding	IDA PMID:9145101 Interaction of Hsp70 chaperones with substrates.	MODIFY	Summary: Rudiger et al. (1997) characterized DnaK interaction with peptide substrates, defining the substrate-binding motif: DnaK recognizes extended peptide strands composed of hydrophobic residues. This directly demonstrates binding to unfolded protein segments. However, GO:0051082 is now formally obsolete. Reason: GO:0051082 is now formally obsolete (go-ontology#30962). While this paper directly demonstrates DnaK binding to unfolded peptide segments, this binding is mechanistically part of DnaK's foldase activity. The correct replacement is GO:0044183 (protein folding chaperone) or GO:0140662 (ATP-dependent protein folding chaperone). DnaK can also act as a holdase in some contexts (PMID:2203539), but the holdase NTR is pending. Proposed replacements: ATP-dependent protein folding chaperone Supporting Evidence: PMID:9145101 DnaK recognizes extended peptide strands composed of up to five consecutive hydrophobic residues within and positively charged residues outside the substrate binding cavity
GO:0008270 zinc ion binding	IDA PMID:11985624 Systematic search for zinc-binding proteins in Escherichia c...	KEEP AS NON CORE	Summary: Katayama et al. (2002) identified DnaK as a zinc-binding protein in a systematic search for zinc-binding proteins in E. coli using radioactive Zn(II) binding assay. DnaK was among nine newly identified zinc-binding proteins. Reason: The abstract explicitly identifies DnaK in a radioactive Zn(II)-binding screen, so the IDA is supported and should not remain undecided. The physiological role and specificity are unresolved, making zinc binding a non-core biochemical property rather than a central chaperone function. Supporting Evidence: PMID:11985624 nine zinc-binding proteins were newly identified including: acetate kinase (AckA), DnaK, serine hydroxymethyltransferase (GlyA) file:ECOLI/DnaK/DnaK-hypotheses/prediction-zinc-binding/openscientist.md DnaK has only one cysteine (Cys15) in 638 residues and no CXXC / C4 zinc-finger motif
GO:0005737 cytoplasm	HDA PMID:16858726 A complexomic study of Escherichia coli using two-dimensiona...	ACCEPT	Summary: HDA annotation from complexomic study (Lasserre et al. 2006) confirming cytoplasmic localization of DnaK. Reason: Cytoplasm is the established localization of DnaK, consistent with multiple studies.
GO:0016020 membrane	HDA PMID:16858726 A complexomic study of Escherichia coli using two-dimensiona...	KEEP AS NON CORE	Summary: HDA annotation from complexomic study detecting DnaK in membrane fractions. UniProt describes DnaK as a peripheral inner membrane protein (PMID:16079137). This is a secondary localization. Reason: DnaK is primarily cytosolic but is also found associated with membranes as a peripheral protein. This is a secondary localization, not the primary one.

Gene Description

Proposed New Ontology Terms

holdase chaperone activity

Existing Annotations Review

Core Functions

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

Falcon

OpenScientist

📚 Additional Documentation

Notes

Bioreason Rl Predictions

Bioreason Rl Review

📄 View Raw YAML