id: P0A6Y8
gene_symbol: DnaK
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:83333
  label: Escherichia coli (strain K12)
description: 'DnaK is the E. coli HSP70 homolog and the canonical bacterial chaperone.
  It is an ATP-dependent foldase that works in concert with its J-domain co-chaperone
  DnaJ (Hsp40) and nucleotide exchange factor GrpE to assist de novo protein folding
  and repair heat-damaged proteins. DnaK undergoes ATP-driven conformational cycles:
  ATP-bound DnaK has an open substrate-binding domain with fast on/off rates; ATP
  hydrolysis (stimulated by DnaJ and substrate) closes the lid and stabilizes substrate
  binding; GrpE-catalyzed ADP release and ATP rebinding triggers substrate release
  for folding. Multiple rounds of this cycle are required for efficient folding of
  many substrates (PMID:7937953). DnaK also functions as a holdase under some conditions,
  protecting proteins from aggregation in an ATP-independent manner (PMID:2203539).
  It cooperates with trigger factor in chaperoning nascent polypeptides (PMID:10380927),
  and collaborates with ClpB (Hsp100) in disaggregation of protein aggregates. DnaK
  also plays a regulatory role by binding and inactivating the heat shock transcription
  factor sigma32 (RpoH) through chaperone-mediated feedback (PMID:8599944). Additionally,
  DnaK is essential for phage lambda DNA replication and participates in chromosomal
  DNA replication via interaction with DnaA.'
existing_annotations:
- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.
    action: ACCEPT
    reason: Core enzymatic activity of DnaK. ATP hydrolysis drives the conformational
      cycle essential for chaperone function. Well-documented experimentally (PMID:7776367,
      PMID:7937953).
    supported_by:
    - reference_id: PMID:7776367
      supporting_text: DnaK ATPase was stimulated by substrates (ninefold) and DnaJ
        (13-fold) through stimulation of the rate limiting step, gamma-phosphate cleavage
    - reference_id: PMID:7937953
      supporting_text: upon interaction with luciferase-DnaJ, DnaK hydrolyzes its
        bound ATP, resulting in the formation of a stable luciferase-DnaK-DnaJ complex
- term:
    id: GO:0031072
    label: heat shock protein binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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).
    action: ACCEPT
    reason: DnaK forms functional complexes with multiple heat shock proteins including
      DnaJ, GrpE, HtpG, and ClpB. This is a well-established feature of the HSP70
      chaperone system.
    supported_by:
    - reference_id: PMID:9103205
      supporting_text: Crystal structure of the nucleotide exchange factor GrpE bound
        to the ATPase domain of the molecular chaperone DnaK
    - reference_id: PMID:21525416
      supporting_text: Results indicate that E. coli Hsp90 and DnaK interact in vivo
        and in vitro
- term:
    id: GO:0044183
    label: protein folding chaperone
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:7937953
      supporting_text: Several rounds of ATP-dependent interaction with DnaK and DnaJ
        are required for fully efficient folding
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: DnaK is predominantly a cytosolic protein. This is supported by multiple
      proteomic studies (PMID:15911532, PMID:18304323) and IBA phylogenetic inference.
    action: ACCEPT
    reason: Well-established localization for DnaK, confirmed by both IDA and IBA
      evidence.
- term:
    id: GO:0042026
    label: protein refolding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    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).
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:7900997
      supporting_text: DnaK, DnaJ and GrpE did not prevent luciferase inactivation,
        but were essential for its reactivation
    - reference_id: PMID:2203539
      supporting_text: heat-inactivated and aggregated RNA polymerase is both disaggregated
        and reactivated following simultaneous incubation with DnaK protein and hydrolyzable
        ATP
- term:
    id: GO:0045892
    label: negative regulation of DNA-templated transcription
  evidence_type: IEA
  original_reference_id: GO_REF:0000108
  review:
    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.
    action: ACCEPT
    reason: Logically sound inference from the experimentally validated sigma factor
      antagonist activity (GO:0016989). DnaK-mediated sequestration of sigma32 represses
      heat shock gene transcription.
    supported_by:
    - reference_id: PMID:8599944
      supporting_text: DnaK and DnaJ cooperatively inhibit sigma32 activity in heat
        shock gene transcription
- term:
    id: GO:0000166
    label: nucleotide binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    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.
    action: ACCEPT
    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.
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    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.
    action: ACCEPT
    reason: Correct annotation. ATP binding is a core feature of DnaK's N-terminal
      nucleotide-binding domain. Redundant with IDA-supported annotations but acceptable.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    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.
    action: ACCEPT
    reason: Correct localization. Broader than cytosol (GO:0005829) but acceptable
      as IEA.
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
- term:
    id: GO:0006260
    label: DNA replication
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
- term:
    id: GO:0006457
    label: protein folding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    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).
    action: ACCEPT
    reason: Protein folding is the core biological process in which DnaK participates.
      This IEA is consistent with the extensive experimental evidence.
- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: IEA annotation from InterPro (IPR013126, Hsp_70_fam). Duplicates the
      IBA annotation for the same term. DnaK has well-characterized intrinsic ATPase
      activity.
    action: ACCEPT
    reason: Correct. Duplicate of the IBA annotation but from a different evidence
      source. ATP hydrolysis is central to DnaK function.
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: IEA annotation from InterPro (IPR012725). GO:0051082 is proposed for
      obsoletion (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.
    action: MODIFY
    reason: GO:0051082 is proposed for obsoletion. 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_replacement_terms:
    - id: GO:0044183
      label: protein folding chaperone
    supported_by:
    - reference_id: PMID:7937953
      supporting_text: 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
- term:
    id: GO:0051087
    label: protein-folding chaperone binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    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).
    action: ACCEPT
    reason: Correct. DnaK physically interacts with multiple protein-folding chaperones
      as part of its functional cycle.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:10521435
  review:
    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.
    action: MODIFY
    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_replacement_terms:
    - id: GO:0051087
      label: protein-folding chaperone binding
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15690043
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    reason: Large-scale protein interaction study. DnaK as a chaperone interacts with
      many cellular proteins; generic protein binding does not capture the mechanistic
      basis. The specific co-chaperone interactions (DnaJ, GrpE) are better annotated
      with GO:0051087.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16139413
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    reason: DnaK association with the RNA degradosome is likely a chaperone-substrate
      interaction. Generic protein binding is uninformative for a promiscuous chaperone.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16606699
  review:
    summary: IPI from large-scale protein-protein interaction study (Arifuzzaman et
      al. 2006). DnaK interactions with GrpE, HtpG, RpoH, CbpA and others detected.
    action: MARK_AS_OVER_ANNOTATED
    reason: Large-scale interaction screen. DnaK is a chaperone with many interactors.
      GO:0005515 is uninformative. Specific functionally meaningful interactions are
      already captured by more specific terms.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16858726
  review:
    summary: IPI from complexomic study (Maddalo et al. 2006) detecting DnaK interactions
      with GrpE (P09372) and ClpB (P63284) by 2D blue native/SDS-PAGE.
    action: MARK_AS_OVER_ANNOTATED
    reason: DnaK-GrpE and DnaK-ClpB interactions are well-known chaperone system interactions,
      better described by GO:0031072 or GO:0051087 than generic protein binding.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:17357109
  review:
    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.
    action: KEEP_AS_NON_CORE
    reason: Xenologous interaction with human HLA-DR. While demonstrating peptide-binding
      capacity of DnaK, this does not represent a native E. coli function.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:17968012
  review:
    summary: IPI with RpoH/sigma32 (P0AGB3). Guisbert et al. (2008) analyzed sigma32
      mutants defective in chaperone-mediated feedback control. DnaK binding to sigma32
      is a central regulatory mechanism of the heat shock response.
    action: MODIFY
    reason: DnaK-sigma32 interaction is a functionally important regulatory interaction,
      better captured by GO:0016989 (sigma factor antagonist activity) which DnaK
      already has. GO:0005515 is uninformative.
    proposed_replacement_terms:
    - id: GO:0016989
      label: sigma factor antagonist activity
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:18394994
  review:
    summary: IPI with DnaJ (P08622). Lin et al. (2008) studied chaperonin-assisted
      folding and DnaK-DnaJ cooperation. Functionally meaningful co-chaperone interaction.
    action: MARK_AS_OVER_ANNOTATED
    reason: DnaK-DnaJ interaction is already captured by GO:0051087 (protein-folding
      chaperone binding). Generic protein binding is uninformative.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19439666
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    reason: DnaK-DnaJ interaction already captured by more specific terms. This study's
      main contribution is structural understanding of the DnaK-ADP-substrate complex.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19698713
  review:
    summary: IPI with ClpB (P63284). Winkler 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.
    action: MODIFY
    reason: DnaK-ClpB interaction is a functionally meaningful chaperone-chaperone
      interaction for protein disaggregation, better captured by GO:0031072 (heat
      shock protein binding).
    proposed_replacement_terms:
    - id: GO:0031072
      label: heat shock protein binding
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21474779
  review:
    summary: IPI with ClpB (P63284). Zietkiewicz et al. (2011) studied species-specific
      collaboration of Hsp70 and Hsp100 in thermotolerance and protein disaggregation.
    action: MARK_AS_OVER_ANNOTATED
    reason: DnaK-ClpB interaction for disaggregation is already captured by more specific
      terms. GO:0005515 is uninformative.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:22065753
  review:
    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.
    action: MARK_AS_OVER_ANNOTATED
    reason: DnaK-DnaJ interaction is a well-characterized co-chaperone interaction
      already annotated with GO:0051087. GO:0005515 adds nothing informative.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:23160352
  review:
    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.
    action: MODIFY
    reason: Functionally important DnaK-ClpB interaction for disaggregation activation.
      Better captured by GO:0031072 (heat shock protein binding).
    proposed_replacement_terms:
    - id: GO:0031072
      label: heat shock protein binding
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:24561554
  review:
    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).
    action: MARK_AS_OVER_ANNOTATED
    reason: Large-scale interaction screen. DnaK-HtpG and DnaK-CbpA are known chaperone
      interactions better captured by specific terms. GO:0005515 is uninformative.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:26545493
  review:
    summary: IPI with RpoH/sigma32 (P0AGB3). Masser et al. (2015) studied the GroEL-to-DnaK
      chaperone network behind sigma32 stability modulation. The DnaK-sigma32 interaction
      is a key regulatory mechanism.
    action: MODIFY
    reason: DnaK-sigma32 interaction for heat shock regulation is better captured
      by GO:0016989 (sigma factor antagonist activity).
    proposed_replacement_terms:
    - id: GO:0016989
      label: sigma factor antagonist activity
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:9103205
  review:
    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.
    action: MODIFY
    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_replacement_terms:
    - id: GO:0051087
      label: protein-folding chaperone binding
    supported_by:
    - reference_id: PMID:9103205
      supporting_text: A dimer of GrpE binds asymmetrically to a single molecule of
        DnaK
- term:
    id: GO:0009408
    label: response to heat
  evidence_type: IDA
  original_reference_id: PMID:7023474
  review:
    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.
    action: ACCEPT
    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.
- term:
    id: GO:0009408
    label: response to heat
  evidence_type: IDA
  original_reference_id: PMID:7900997
  review:
    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.
    action: ACCEPT
    reason: Direct demonstration of DnaK function in the heat stress response, specifically
      repairing heat-damaged proteins.
    supported_by:
    - reference_id: PMID:7900997
      supporting_text: DnaK, DnaJ and GrpE did not prevent luciferase inactivation,
        but were essential for its reactivation
- term:
    id: GO:0009408
    label: response to heat
  evidence_type: IEP
  original_reference_id: PMID:8349564
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:8349564
      supporting_text: 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)
- term:
    id: GO:0034620
    label: cellular response to unfolded protein
  evidence_type: IDA
  original_reference_id: PMID:2203539
  review:
    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.
    action: ACCEPT
    reason: DnaK is a central effector of the cellular response to unfolded proteins,
      both preventing aggregation and reactivating misfolded/aggregated proteins.
    supported_by:
    - reference_id: PMID:2203539
      supporting_text: 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
- term:
    id: GO:0034620
    label: cellular response to unfolded protein
  evidence_type: IDA
  original_reference_id: PMID:7900997
  review:
    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.
    action: ACCEPT
    reason: DnaK is essential for the cellular response to unfolded/denatured proteins.
    supported_by:
    - reference_id: PMID:7900997
      supporting_text: DnaJ associated with denatured luciferase, targeted DnaK to
        the substrate and co-operated with DnaK to prevent luciferase aggregation
        at 42 degrees C
- term:
    id: GO:0043335
    label: protein unfolding
  evidence_type: IDA
  original_reference_id: PMID:20953191
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:20953191
      supporting_text: 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
- term:
    id: GO:0140662
    label: ATP-dependent protein folding chaperone
  evidence_type: IDA
  original_reference_id: PMID:2203539
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:2203539
      supporting_text: heat-inactivated and aggregated RNA polymerase is both disaggregated
        and reactivated following simultaneous incubation with DnaK protein and hydrolyzable
        ATP
- term:
    id: GO:0140662
    label: ATP-dependent protein folding chaperone
  evidence_type: IDA
  original_reference_id: PMID:7937953
  review:
    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.
    action: ACCEPT
    reason: Definitive demonstration of DnaK's ATP-dependent chaperone cycle. This
      paper established the mechanistic framework for the DnaK system.
    supported_by:
    - reference_id: PMID:7937953
      supporting_text: 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
- term:
    id: GO:1990169
    label: stress response to copper ion
  evidence_type: IMP
  original_reference_id: PMID:35289645
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
- term:
    id: GO:0051087
    label: protein-folding chaperone binding
  evidence_type: IPI
  original_reference_id: PMID:21525416
  review:
    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.
    action: ACCEPT
    reason: DnaK-HtpG (Hsp90) interaction is a functionally relevant chaperone-chaperone
      binding event important for client remodeling. GO:0051087 appropriately captures
      this.
    supported_by:
    - reference_id: PMID:21525416
      supporting_text: 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
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:30442809
  review:
    summary: IPI with OmpA (P0A910) from native membrane mass spectrometry study (Chorev
      et al. 2018). DnaK was found associated with membrane protein complexes.
    action: MARK_AS_OVER_ANNOTATED
    reason: DnaK association with membrane protein OmpA likely reflects chaperone
      function at the membrane. GO:0005515 is uninformative for a general chaperone.
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IDA
  original_reference_id: PMID:9103205
  review:
    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.
    action: ACCEPT
    reason: ATP binding is a core function of DnaK's N-terminal nucleotide-binding
      domain (NBD). Well-supported by structural and biochemical data.
    supported_by:
    - reference_id: PMID:9103205
      supporting_text: The structure of the nucleotide-free ATPase domain in complex
        with GrpE resembles closely that of the nucleotide-bound mammalian Hsp70 homolog
- term:
    id: GO:0006457
    label: protein folding
  evidence_type: IDA
  original_reference_id: PMID:9103205
  review:
    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.
    action: ACCEPT
    reason: Protein folding is the core biological process of DnaK. While this specific
      paper is primarily structural, it provides context for the nucleotide cycle
      that drives folding.
- term:
    id: GO:0032991
    label: protein-containing complex
  evidence_type: IDA
  original_reference_id: PMID:9103205
  review:
    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.
    action: ACCEPT
    reason: DnaK forms well-characterized complexes with GrpE (crystallized) and DnaJ.
      The DnaK-GrpE complex is a bona fide protein-containing complex.
    supported_by:
    - reference_id: PMID:9103205
      supporting_text: A dimer of GrpE binds asymmetrically to a single molecule of
        DnaK
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IDA
  original_reference_id: PMID:9103205
  review:
    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 proposed for obsoletion, and DnaK's function is better
      described as ATP-dependent protein folding chaperone (GO:0140662).
    action: MODIFY
    reason: GO:0051082 is proposed for obsoletion (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_replacement_terms:
    - id: GO:0140662
      label: ATP-dependent protein folding chaperone
- term:
    id: GO:0051087
    label: protein-folding chaperone binding
  evidence_type: IPI
  original_reference_id: PMID:9103205
  review:
    summary: IPI with DnaJ (P08622) from the GrpE-DnaK crystal structure study. While
      the primary focus is GrpE-DnaK, DnaJ interaction is discussed in the context
      of the chaperone cycle.
    action: ACCEPT
    reason: DnaK binding to co-chaperones DnaJ and GrpE is a core functional interaction.
      GO:0051087 appropriately captures chaperone-chaperone binding.
- term:
    id: GO:0065003
    label: protein-containing complex assembly
  evidence_type: IDA
  original_reference_id: PMID:9103205
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
- term:
    id: GO:0016234
    label: inclusion body
  evidence_type: IDA
  original_reference_id: PMID:15866952
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:15866952
      supporting_text: chaperones DnaK and GroEL have been identified at the solvent-exposed
        surface of bacterial inclusion bodies and entrapped within these aggregates,
        respectively
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:2522091
  review:
    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.
    action: MODIFY
    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_replacement_terms:
    - id: GO:0051087
      label: protein-folding chaperone binding
    supported_by:
    - reference_id: PMID:2522091
      supporting_text: Coimmunoprecipitation of DnaK+ and GrpE+ proteins from cell
        lysates with anti-DnaK antibodies demonstrated their interaction in vitro
- term:
    id: GO:0016989
    label: sigma factor antagonist activity
  evidence_type: IDA
  original_reference_id: PMID:8599944
  review:
    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.
    action: ACCEPT
    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 non-core but well-characterized MF of DnaK. The chaperone-mediated
      feedback control of the heat shock response depends on this activity.
    supported_by:
    - reference_id: PMID:8599944
      supporting_text: DnaK and DnaJ cooperatively inhibit sigma32 activity in heat
        shock gene transcription and GrpE partially reverses this inhibition
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IDA
  original_reference_id: PMID:15911532
  review:
    summary: IDA localization study (Sato et al. 2005) confirming DnaK is present
      in the E. coli cytosol under different growth conditions.
    action: ACCEPT
    reason: Cytosol is the primary localization of DnaK, confirmed by multiple independent
      studies.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IDA
  original_reference_id: PMID:18304323
  review:
    summary: IDA from protein abundance profiling of the E. coli cytosol (Ishihama
      et al. 2008). DnaK is one of the most abundant cytosolic proteins.
    action: ACCEPT
    reason: Confirms cytosolic localization. DnaK is one of the most abundant proteins
      in the E. coli cytosol.
    supported_by:
    - reference_id: PMID:18304323
      supporting_text: 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
- term:
    id: GO:0044183
    label: protein folding chaperone
  evidence_type: IDA
  original_reference_id: PMID:10380927
  review:
    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.
    action: ACCEPT
    reason: Definitive demonstration of DnaK as a de novo protein folding chaperone
      for nascent polypeptides. This is a core molecular function.
    supported_by:
    - reference_id: PMID:10380927
      supporting_text: 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
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IDA
  original_reference_id: PMID:7776367
  review:
    summary: McCarty et al. (1995) characterized the ATP hydrolysis cycle of DnaK,
      showing that ATP-bound DnaK is the primary form initiating substrate interaction.
    action: ACCEPT
    reason: Core function. ATP binding to DnaK's NBD drives its conformational cycle.
      This paper provided detailed kinetic characterization of the nucleotide cycle.
    supported_by:
    - reference_id: PMID:7776367
      supporting_text: The rapid binding kinetics lead to the conclusion that ATP-bound
        DnaK is the primary form initiating interaction with substrates for chaperone
        activity
- term:
    id: GO:0043531
    label: ADP binding
  evidence_type: IDA
  original_reference_id: PMID:19439666
  review:
    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.
    action: ACCEPT
    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.
    supported_by:
    - reference_id: PMID:19439666
      supporting_text: an experimental structure for wild-type, full-length DnaK,
        complexed with the peptide NRLLLTG and with ADP
- term:
    id: GO:0043531
    label: ADP binding
  evidence_type: IDA
  original_reference_id: PMID:7776367
  review:
    summary: McCarty et al. (1995) characterized DnaK's nucleotide binding properties,
      including ADP binding and its role in the functional cycle.
    action: ACCEPT
    reason: ADP binding is essential for the DnaK chaperone cycle. GrpE stimulates
      ADP release, which is a key regulatory step.
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IDA
  original_reference_id: PMID:9145101
  review:
    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 proposed for obsoletion.'
    action: MODIFY
    reason: GO:0051082 is proposed for obsoletion (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_replacement_terms:
    - id: GO:0140662
      label: ATP-dependent protein folding chaperone
    supported_by:
    - reference_id: PMID:9145101
      supporting_text: DnaK recognizes extended peptide strands composed of up to
        five consecutive hydrophobic residues within and positively charged residues
        outside the substrate binding cavity
- term:
    id: GO:0008270
    label: zinc ion binding
  evidence_type: IDA
  original_reference_id: PMID:11985624
  review:
    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.
    action: UNDECIDED
    reason: The zinc-binding activity was detected in a systematic proteome-wide screen
      using radioactive zinc. While DnaK was identified, the biological significance
      of zinc binding to DnaK is unclear. DnaK does not contain a canonical zinc-finger
      or zinc-binding motif. This may represent adventitious metal binding rather
      than a biologically relevant function. There is no known role for zinc in DnaK's
      chaperone mechanism.
    supported_by:
    - reference_id: PMID:11985624
      supporting_text: 'nine zinc-binding proteins were newly identified including:
        acetate kinase (AckA), DnaK, serine hydroxymethyltransferase (GlyA)'
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: HDA
  original_reference_id: PMID:16858726
  review:
    summary: HDA annotation from complexomic study (Maddalo et al. 2006) confirming
      cytoplasmic localization of DnaK.
    action: ACCEPT
    reason: Cytoplasm is the established localization of DnaK, consistent with multiple
      studies.
- term:
    id: GO:0016020
    label: membrane
  evidence_type: HDA
  original_reference_id: PMID:16858726
  review:
    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.
    action: KEEP_AS_NON_CORE
    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.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: GO_REF:0000108
  title: Automatic assignment of GO terms using logical inference, based on on inter-ontology
    links
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:10380927
  title: 'Polypeptide flux through bacterial Hsp70: DnaK cooperates with trigger factor
    in chaperoning nascent chains.'
  findings:
  - statement: DnaK functions as a de novo protein folding chaperone, transiently
      associating with nascent polypeptides under nonstress conditions.
    supporting_text: under nonstress conditions DnaK transiently associates with a
      wide variety of nascent and newly synthesized polypeptides, with a preference
      for chains larger than 30 kDa
- id: PMID:10521435
  title: Structural features required for the interaction of the Hsp70 molecular chaperone
    DnaK with its cochaperone DnaJ.
  findings: []
- id: PMID:11985624
  title: Systematic search for zinc-binding proteins in Escherichia coli.
  findings:
  - statement: DnaK identified as a zinc-binding protein in systematic proteome-wide
      screen. Biological significance unclear.
    supporting_text: 'nine zinc-binding proteins were newly identified including:
      acetate kinase (AckA), DnaK, serine hydroxymethyltransferase (GlyA)'
- id: PMID:15690043
  title: Interaction network containing conserved and essential protein complexes
    in Escherichia coli.
  findings: []
- id: PMID:15866952
  title: Localization of chaperones DnaK and GroEL in bacterial inclusion bodies.
  findings:
  - statement: DnaK localizes to the solvent-exposed surface of bacterial inclusion
      bodies.
    supporting_text: chaperones DnaK and GroEL have been identified at the solvent-exposed
      surface of bacterial inclusion bodies and entrapped within these aggregates,
      respectively
- id: PMID:15911532
  title: Localization, annotation, and comparison of the Escherichia coli K-12 proteome
    under two states of growth.
  findings: []
- id: PMID:16139413
  title: Analysis of the Escherichia coli RNA degradosome composition by a proteomic
    approach.
  findings: []
- id: PMID:16606699
  title: Large-scale identification of protein-protein interaction of Escherichia
    coli K-12.
  findings: []
- id: PMID:16858726
  title: A complexomic study of Escherichia coli using two-dimensional blue native/SDS
    polyacrylamide gel electrophoresis.
  findings: []
- id: PMID:17357109
  title: '70-kDa heat shock proteins: specific interactions with HLA-DR molecules
    and their peptide fragments.'
  findings: []
- id: PMID:17968012
  title: Analysis of sigma32 mutants defective in chaperone-mediated feedback control
    reveals unexpected complexity of the heat shock response.
  findings: []
- id: PMID:18304323
  title: Protein abundance profiling of the Escherichia coli cytosol.
  findings: []
- id: PMID:18394994
  title: Monitoring protein conformation along the pathway of chaperonin-assisted
    folding.
  findings: []
- id: PMID:19439666
  title: Solution conformation of wild-type E. coli Hsp70 (DnaK) chaperone complexed
    with ADP and substrate.
  findings:
  - statement: Solution structure of full-length DnaK in ADP-substrate bound state.
      NBD and SBD are loosely linked with dynamic relative orientation.
    supporting_text: an experimental structure for wild-type, full-length DnaK, complexed
      with the peptide NRLLLTG and with ADP
- id: PMID:19698713
  title: DnaK-mediated association of ClpB to protein aggregates. A bichaperone network
    at the aggregate surface.
  findings:
  - statement: DnaK mediates recruitment of ClpB disaggregase to protein aggregates.
    supporting_text: ClpB binding strictly depends on previous DnaK association with
      the aggregate... DnaK mediates ClpB interaction with the aggregate surface
- id: PMID:20953191
  title: The kinetic parameters and energy cost of the Hsp70 chaperone as a polypeptide
    unfoldase.
  findings:
  - statement: DnaK functions as a polypeptide unfoldase, consuming 5 ATPs to unfold
      one misfolded protein into a spontaneously refoldable intermediate.
    supporting_text: 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
- id: PMID:21474779
  title: Species-specific collaboration of heat shock proteins (Hsp) 70 and 100 in
    thermotolerance and protein disaggregation.
  findings: []
- id: PMID:21525416
  title: Heat shock protein 90 from Escherichia coli collaborates with the DnaK chaperone
    system in client protein remodeling.
  findings:
  - statement: E. coli Hsp90 (HtpG) and DnaK interact and collaborate in client protein
      remodeling.
    supporting_text: 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
- id: PMID:2203539
  title: The E. coli dnaK gene product, the hsp70 homolog, can reactivate heat-inactivated
    RNA polymerase in an ATP hydrolysis-dependent manner.
  findings:
  - statement: DnaK protects RNA polymerase from heat inactivation (ATP-independent
      holdase) and reactivates aggregated RNA polymerase (ATP-dependent foldase/disaggregase).
    supporting_text: 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
- id: PMID:22065753
  title: Heat shock protein 70 kDa chaperone/DnaJ cochaperone complex employs an unusual
    dynamic interface.
  findings: []
- id: PMID:23160352
  title: Hsp70 proteins bind Hsp100 regulatory M domains to activate AAA+ disaggregase
    at aggregate surfaces.
  findings:
  - statement: DnaK activates ClpB disaggregase by binding its regulatory M domain.
    supporting_text: DnaK directly binds M-domain motif 2, increasing ClpB ATPase
      activity to unleash high ClpB threading power
- id: PMID:24561554
  title: The binary protein-protein interaction landscape of Escherichia coli.
  findings: []
- id: PMID:2522091
  title: Escherichia coli DnaK and GrpE heat shock proteins interact both in vivo
    and in vitro.
  findings:
  - statement: DnaK and GrpE functionally interact, shown by genetic suppression and
      coimmunoprecipitation.
    supporting_text: Coimmunoprecipitation of DnaK+ and GrpE+ proteins from cell lysates
      with anti-DnaK antibodies demonstrated their interaction in vitro
- id: PMID:26545493
  title: GroEL to DnaK chaperone network behind the stability modulation of σ(32)
    at physiological temperature in Escherichia coli.
  findings:
  - statement: GroEL acts upstream of DnaK in an ordered network that modulates sigma32
      stability at physiological temperature.
    supporting_text: neither DnaK nor GroEL singly can modulate sigma(32) stability
      in vivo; there is an ordered network between them, where GroEL acts upstream
      of DnaK
- id: PMID:30442809
  title: Protein assemblies ejected directly from native membranes yield complexes
    for mass spectrometry.
  findings: []
- id: PMID:35289645
  title: Copper Induces Protein Aggregation, a Toxic Process Compensated by Molecular
    Chaperones.
  findings:
  - statement: Copper induces protein aggregation and DnaK compensates for this toxicity.
    supporting_text: coli strains lacking the cytosolic chaperone DnaK or trigger
      factor are highly sensitive to copper stress
- id: PMID:7023474
  title: Positive regulatory gene for temperature-controlled proteins in Escherichia
    coli.
  findings: []
- id: PMID:7776367
  title: The role of ATP in the functional cycle of the DnaK chaperone system.
  findings:
  - statement: Detailed kinetic characterization of DnaK's ATPase cycle. ATP-bound
      DnaK initiates substrate interaction; DnaJ stimulates ATP hydrolysis to stabilize
      substrate binding.
    supporting_text: DnaK ATPase was stimulated by substrates (ninefold) and DnaJ
      (13-fold) through stimulation of the rate limiting step, gamma-phosphate cleavage
- id: PMID:7900997
  title: DnaK, DnaJ and GrpE form a cellular chaperone machinery capable of repairing
    heat-induced protein damage.
  findings:
  - statement: DnaK/DnaJ/GrpE system repairs heat-damaged luciferase both in vivo
      and in vitro. DnaJ targets DnaK to denatured substrates. ATP required for reactivation.
    supporting_text: DnaK, DnaJ and GrpE did not prevent luciferase inactivation,
      but were essential for its reactivation
- id: PMID:7937953
  title: The ATP hydrolysis-dependent reaction cycle of the Escherichia coli Hsp70
    system DnaK, DnaJ, and GrpE.
  findings:
  - statement: 'Defined the four-step chaperone cycle: substrate-DnaJ interaction,
      DnaK ATP hydrolysis and complex formation, GrpE-mediated ADP release, ATP-triggered
      substrate release. Multiple rounds needed for efficient folding.'
    supporting_text: Several rounds of ATP-dependent interaction with DnaK and DnaJ
      are required for fully efficient folding
- id: PMID:8349564
  title: Characterization of twenty-six new heat shock genes of Escherichia coli.
  findings: []
- id: PMID:8599944
  title: A cycle of binding and release of the DnaK, DnaJ and GrpE chaperones regulates
    activity of the Escherichia coli heat shock transcription factor sigma32.
  findings:
  - statement: DnaK/DnaJ bind free sigma32 and inhibit its transcriptional activity.
      GrpE/ATP drive release cycle. Central regulatory element of the heat shock response.
    supporting_text: DnaK and DnaJ cooperatively inhibit sigma32 activity in heat
      shock gene transcription and GrpE partially reverses this inhibition
- id: PMID:9103205
  title: Crystal structure of the nucleotide exchange factor GrpE bound to the ATPase
    domain of the molecular chaperone DnaK.
  findings:
  - statement: GrpE dimer binds asymmetrically to one DnaK molecule. Conformational
      change in DnaK NBD inconsistent with tight nucleotide binding explains GrpE's
      exchange mechanism.
    supporting_text: A dimer of GrpE binds asymmetrically to a single molecule of
      DnaK
- id: PMID:9145101
  title: Interaction of Hsp70 chaperones with substrates.
  findings:
  - statement: DnaK recognizes extended peptide strands with hydrophobic core and
      flanking positive charges. Defines substrate-binding specificity of Hsp70.
    supporting_text: DnaK recognizes extended peptide strands composed of up to five
      consecutive hydrophobic residues within and positively charged residues outside
      the substrate binding cavity
core_functions:
- molecular_function:
    id: GO:0140662
    label: ATP-dependent protein folding chaperone
  description: DnaK is the E. coli HSP70 homolog that functions as an ATP-dependent
    protein folding chaperone (foldase). It binds unfolded polypeptide segments, undergoes
    ATP hydrolysis- driven conformational changes (with DnaJ and GrpE co-chaperones),
    and releases substrates to allow folding. Multiple rounds of binding and release
    are required for efficient folding of most substrates (PMID:7937953). DnaK also
    protects proteins from heat inactivation (holdase function, ATP-independent; PMID:2203539)
    and cooperates with trigger factor to chaperone nascent polypeptides (PMID:10380927).
  directly_involved_in:
  - id: GO:0042026
    label: protein refolding
  - id: GO:0006457
    label: protein folding
  - id: GO:0034620
    label: cellular response to unfolded protein
  - id: GO:0009408
    label: response to heat
  - id: GO:0043335
    label: protein unfolding
  locations:
  - id: GO:0005829
    label: cytosol
  - id: GO:0016234
    label: inclusion body
  supported_by:
  - reference_id: PMID:7937953
    supporting_text: Several rounds of ATP-dependent interaction with DnaK and DnaJ
      are required for fully efficient folding
  - reference_id: PMID:10380927
    supporting_text: DnaK transiently associates with a wide variety of nascent and
      newly synthesized polypeptides, with a preference for chains larger than 30
      kDa
- molecular_function:
    id: GO:0016989
    label: sigma factor antagonist activity
  description: DnaK inhibits sigma32 (RpoH) transcriptional activity by direct binding,
    constituting the chaperone-mediated negative feedback loop of the heat shock response.
    DnaK and DnaJ cooperatively sequester free sigma32, preventing its association
    with RNA polymerase. GrpE and ATP drive the release cycle (PMID:8599944).
  directly_involved_in:
  - id: GO:0045892
    label: negative regulation of DNA-templated transcription
  locations:
  - id: GO:0005829
    label: cytosol
  supported_by:
  - reference_id: PMID:8599944
    supporting_text: DnaK and DnaJ cooperatively inhibit sigma32 activity in heat
      shock gene transcription
suggested_questions:
- question: How does DnaK's holdase activity (ATP-independent aggregation prevention)
    relate to its foldase activity? Should both be annotated once the holdase NTR
    is created?
- question: Does DnaK have a genuine disaggregase function independent of ClpB, or
    is it solely a co-factor for ClpB-mediated disaggregation?
- question: Is the zinc-binding detected by Katayama et al. (PMID:11985624) biologically
    relevant or adventitious?