Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
Electronic Gene Ontology annotations created by ARBA machine learning models
Combined Automated Annotation using Multiple IEA Methods
Polypeptide flux through bacterial Hsp70: DnaK cooperates with trigger factor in chaperoning nascent chains.
-
DnaK functions as a de novo protein folding chaperone, transiently associating with nascent polypeptides under nonstress conditions.
"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"
Structural features required for the interaction of the Hsp70 molecular chaperone DnaK with its cochaperone DnaJ.
Systematic search for zinc-binding proteins in Escherichia coli.
-
DnaK identified as a zinc-binding protein in systematic proteome-wide screen. Biological significance unclear.
"nine zinc-binding proteins were newly identified including: acetate kinase (AckA), DnaK, serine hydroxymethyltransferase (GlyA)"
Interaction network containing conserved and essential protein complexes in Escherichia coli.
Localization of chaperones DnaK and GroEL in bacterial inclusion bodies.
-
DnaK localizes to the solvent-exposed surface of bacterial inclusion bodies.
"chaperones DnaK and GroEL have been identified at the solvent-exposed surface of bacterial inclusion bodies and entrapped within these aggregates, respectively"
Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth.
Analysis of the Escherichia coli RNA degradosome composition by a proteomic approach.
Large-scale identification of protein-protein interaction of Escherichia coli K-12.
A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis.
70-kDa heat shock proteins: specific interactions with HLA-DR molecules and their peptide fragments.
Analysis of sigma32 mutants defective in chaperone-mediated feedback control reveals unexpected complexity of the heat shock response.
Protein abundance profiling of the Escherichia coli cytosol.
Monitoring protein conformation along the pathway of chaperonin-assisted folding.
Solution conformation of wild-type E. coli Hsp70 (DnaK) chaperone complexed with ADP and substrate.
-
Solution structure of full-length DnaK in ADP-substrate bound state. NBD and SBD are loosely linked with dynamic relative orientation.
"an experimental structure for wild-type, full-length DnaK, complexed with the peptide NRLLLTG and with ADP"
DnaK-mediated association of ClpB to protein aggregates. A bichaperone network at the aggregate surface.
-
DnaK mediates recruitment of ClpB disaggregase to protein aggregates.
"ClpB binding strictly depends on previous DnaK association with the aggregate... DnaK mediates ClpB interaction with the aggregate surface"
The kinetic parameters and energy cost of the Hsp70 chaperone as a polypeptide unfoldase.
-
DnaK functions as a polypeptide unfoldase, consuming 5 ATPs to unfold one misfolded protein into a spontaneously refoldable intermediate.
"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"
Species-specific collaboration of heat shock proteins (Hsp) 70 and 100 in thermotolerance and protein disaggregation.
Heat shock protein 90 from Escherichia coli collaborates with the DnaK chaperone system in client protein remodeling.
-
E. coli Hsp90 (HtpG) and DnaK interact and collaborate in client protein remodeling.
"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"
The E. coli dnaK gene product, the hsp70 homolog, can reactivate heat-inactivated RNA polymerase in an ATP hydrolysis-dependent manner.
-
DnaK protects RNA polymerase from heat inactivation (ATP-independent holdase) and reactivates aggregated RNA polymerase (ATP-dependent foldase/disaggregase).
"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"
Heat shock protein 70 kDa chaperone/DnaJ cochaperone complex employs an unusual dynamic interface.
Hsp70 proteins bind Hsp100 regulatory M domains to activate AAA+ disaggregase at aggregate surfaces.
-
DnaK activates ClpB disaggregase by binding its regulatory M domain.
"DnaK directly binds M-domain motif 2, increasing ClpB ATPase activity to unleash high ClpB threading power"
The binary protein-protein interaction landscape of Escherichia coli.
Escherichia coli DnaK and GrpE heat shock proteins interact both in vivo and in vitro.
-
DnaK and GrpE functionally interact, shown by genetic suppression and coimmunoprecipitation.
"Coimmunoprecipitation of DnaK+ and GrpE+ proteins from cell lysates with anti-DnaK antibodies demonstrated their interaction in vitro"
GroEL to DnaK chaperone network behind the stability modulation of σ(32) at physiological temperature in Escherichia coli.
-
GroEL acts upstream of DnaK in an ordered network that modulates sigma32 stability at physiological temperature.
"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"
Protein assemblies ejected directly from native membranes yield complexes for mass spectrometry.
Copper Induces Protein Aggregation, a Toxic Process Compensated by Molecular Chaperones.
Positive regulatory gene for temperature-controlled proteins in Escherichia coli.
The role of ATP in the functional cycle of the DnaK chaperone system.
-
Detailed kinetic characterization of DnaK's ATPase cycle. ATP-bound DnaK initiates substrate interaction; DnaJ stimulates ATP hydrolysis to stabilize substrate binding.
"DnaK ATPase was stimulated by substrates (ninefold) and DnaJ (13-fold) through stimulation of the rate limiting step, gamma-phosphate cleavage"
DnaK, DnaJ and GrpE form a cellular chaperone machinery capable of repairing heat-induced protein damage.
-
DnaK/DnaJ/GrpE system repairs heat-damaged luciferase both in vivo and in vitro. DnaJ targets DnaK to denatured substrates. ATP required for reactivation.
"DnaK, DnaJ and GrpE did not prevent luciferase inactivation, but were essential for its reactivation"
The ATP hydrolysis-dependent reaction cycle of the Escherichia coli Hsp70 system DnaK, DnaJ, and GrpE.
-
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.
"Several rounds of ATP-dependent interaction with DnaK and DnaJ are required for fully efficient folding"
Characterization of twenty-six new heat shock genes of Escherichia coli.
A cycle of binding and release of the DnaK, DnaJ and GrpE chaperones regulates activity of the Escherichia coli heat shock transcription factor sigma32.
-
DnaK/DnaJ bind free sigma32 and inhibit its transcriptional activity. GrpE/ATP drive release cycle. Central regulatory element of the heat shock response.
"DnaK and DnaJ cooperatively inhibit sigma32 activity in heat shock gene transcription and GrpE partially reverses this inhibition"
Crystal structure of the nucleotide exchange factor GrpE bound to the ATPase domain of the molecular chaperone DnaK.
-
GrpE dimer binds asymmetrically to one DnaK molecule. Conformational change in DnaK NBD inconsistent with tight nucleotide binding explains GrpE's exchange mechanism.
"A dimer of GrpE binds asymmetrically to a single molecule of DnaK"
Interaction of Hsp70 chaperones with substrates.
-
DnaK recognizes extended peptide strands with hydrophobic core and flanking positive charges. Defines substrate-binding specificity of Hsp70.
"DnaK recognizes extended peptide strands composed of up to five consecutive hydrophobic residues within and positively charged residues outside the substrate binding cavity"
UniProt record for Escherichia coli DnaK (P0A6Y8)
Deep research synthesis for Escherichia coli DnaK
-
Background synthesis of the ATP-driven Hsp70 client-binding cycle, used only as corroboration of the primary literature audit.
"DnaK is an ATP-dependent molecular chaperone"
Unfolded protein binding annotation review project
OpenScientist focused report on DnaK zinc-binding prediction
-
Focused computational-prediction audit finding no canonical zinc-binding motif or structural zinc site in DnaK, qualifying the single Zn-blot IDA row as weak, non-core evidence.
"0/63 DnaK PDB entries contain a ZN ligand"