RegulonDB RegulonDB 10.8: Gene Form
   

dnaK gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

dnaK dnaJ yaaI tpke11 terminator TSS_38 TSS_38 TSS_37 TSS_37 TSS_36 TSS_36 TSS_35 (cluster) TSS_35 (cluster) TSS_34 TSS_34 TSS_33 TSS_33 TSS_32 (cluster) TSS_32 (cluster) TSS_31 (cluster) TSS_31 (cluster) TSS_30 TSS_30 TSS_29 TSS_29 TSS_28 TSS_28 dnaKp3 dnaKp3 TSS_27 TSS_27 dnaKp2 dnaKp2 dnaKp1 dnaKp1 yaaIp2 yaaIp2 yaaIp3 yaaIp3 yaaIp4 yaaIp4 yaaWp3 yaaWp3

Gene      
Name: dnaK    Texpresso search in the literature
Synonym(s): ECK0014, EG10241, b0014, groPAB, groPC, groPF, grpC, grpF, seg
Genome position(nucleotides): 12163 --> 14079 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.12
Reference(s): [1] Saito H., et al., 1977
[2] Yochem J., et al., 1978
External database links:  
ASAP:
 ABE-0000052
CGSC:
 844
ECHOBASE:
 EB0237
MIM:
 182170
MIM:
 616854
OU-MICROARRAY:
 b0014
PortEco:
 dnaK
STRING:
 511145.b0014
COLOMBOS: dnaK


Product      
Name: chaperone protein DnaK
Synonym(s): DnaK, GrpC, GrpF, Hsp70, Seg, heat shock protein 70
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol,inner membrane
Molecular weight: 69.115
Isoelectric point: 4.584
Motif(s):
 
Type Positions Sequence
390 -> 600 LLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLME
455 -> 455 G
560 -> 638 DDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQQHAQQQTAGADASANNAKDDDVVDAEFEEVKDKK
2 -> 638 GKIIGIDLGTTNSCVAIMDGTTPRVLENAEGDRTTPSIIAYTQDGETLVGQPAKRQAVTNPQNTLFAIKRLIGRRFQDEEVQRDVSIMPFKIIAADNGDAWVEVKGQKMAPPQISAEVLKKMKKTAEDYLGEPVTEAVITVPAYFNDAQRQATKDAGRIAGLEVKRIINEPTAAALAYGLDKGTGNRTIAVYDLGGGTFDISIIEIDEVDGEKTFEVLATNGDTHLGGEDFDSRLINYLVEEFKKDQGIDLRNDPLAMQRLKEAAEKAKIELSSAQQTDVNLPYITADATGPKHMNIKVTRAKLESLVEDLVNRSIEPLKVALQDAGLSVSDIDDVILVGGQTRMPMVQKKVAEFFGKEPRKDVNPDEAVAIGAAVQGGVLTGDVKDVLLLDVTPLSLGIETMGGVMTTLIAKNTTIPTKHSQVFSTAEDNQSAVTIHVLQGERKRAADNKSLGQFNLDGINPAPRGMPQIEVTFDIDADGILHVSAKDKNSGKEQKITIKASSGLNEDEIQKMVRDAEANAEADRKFEELVQTRNQGDHLLHSTRKQVEEAGDKLPADDKTAIESALTALETALKGEDKAAIEAKMQELAQVSQKLMEIAQQQHAQQQTAGADASANNAKDDDVVDAEFEEVKDKK
32 -> 32 G

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.4 - chaperoning, repair (refolding)
  5 - cell processes --> 5.1 - cell division
  5 - cell processes --> 5.5 - adaptations --> 5.5.1 - osmotic pressure
Gene Ontology Terms (GO)  
cellular_component GO:0016234 - inclusion body
GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0032991 - protein-containing complex
molecular_function GO:0051787 - misfolded protein binding
GO:0005515 - protein binding
GO:0016887 - ATPase activity
GO:0016989 - sigma factor antagonist activity
GO:0051082 - unfolded protein binding
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0008270 - zinc ion binding
GO:0031072 - heat shock protein binding
GO:0051087 - chaperone binding
GO:0043531 - ADP binding
GO:0044183 - protein folding chaperone
biological_process GO:0006260 - DNA replication
GO:0006457 - protein folding
GO:0009408 - response to heat
GO:0042026 - protein refolding
GO:0065003 - protein-containing complex assembly
GO:0032984 - protein-containing complex disassembly
GO:0051085 - chaperone cofactor-dependent protein refolding
GO:0043335 - protein unfolding
GO:0006986 - response to unfolded protein
GO:0034620 - cellular response to unfolded protein
GO:1903507 - negative regulation of nucleic acid-templated transcription
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[AUP] Assay of unpurified protein
[IGI] Inferred from genetic interaction
[IMP] Inferred from mutant phenotype
Reference(s): [3] Alberts N., et al., 2019
[4] Banecki B., et al., 1996
[5] Barthel TK., et al., 2001
[6] Bauer D., et al., 2018
[7] Bertelsen EB., et al., 2009
[8] Bukau B., et al., 1990
[9] Burkholder WF., et al., 1994
[10] Chorev DS., et al., 2018
[11] Desantis ME., et al., 2014
[12] Deuerling E., et al., 1999
[13] Doyle SM., et al., 2015
[14] Durie CL., et al., 2018
[15] Fernandez-Higuero JA., et al., 2018
[16] Georgopoulos C., et al., 1982
[17] Georgopoulos CP., et al., 1979
[18] Goloubinoff P., et al., 1999
[19] Grudniak AM., et al., 2011
[20] Kadibalban AS., et al., 2016
[21] Kamath-Loeb AS., et al., 1995
[22] Kusukawa N., et al., 1988
[23] Lopez V., et al., 2016
[24] Melkina OE., et al., 2017
[25] Miot M., et al., 2011
[26] Montgomery DL., et al., 1999
[1] Saito H., et al., 1977
[27] Schroder H., et al., 1993
[28] Skowyra D., et al., 1990
[29] Slepenkov SV., et al., 2003
[30] Sugimoto S., et al., 2018
[31] Szabo A., et al., 1994
[32] Teter SA., et al., 1999
[33] Tomoyasu T., et al., 1998
[34] Wild J., et al., 1992
[35] Zolkiewski M., et al., 2016
External database links:  
DIP:
 DIP-35751N
ECOCYC:
 EG10241-MONOMER
ECOLIWIKI:
 b0014
INTERPRO:
 IPR013126
INTERPRO:
 IPR018181
INTERPRO:
 IPR029047
INTERPRO:
 IPR029048
INTERPRO:
 IPR012725
MINT:
 P0A6Y8
PANTHER:
 PTHR19375
PDB:
 3DPP
PDB:
 3DPQ
PDB:
 3QNJ
PDB:
 4B9Q
PDB:
 4E81
PDB:
 4EZN
PDB:
 4EZO
PDB:
 4EZP
PDB:
 4EZQ
PDB:
 4EZR
PDB:
 4EZS
PDB:
 4EZT
PDB:
 4EZU
PDB:
 4EZV
PDB:
 4EZW
PDB:
 4EZY
PDB:
 4EZZ
PDB:
 4F00
PDB:
 4F01
PDB:
 4HY9
PDB:
 4HYB
PDB:
 4JN4
PDB:
 4JNE
PDB:
 4JNF
PDB:
 4JWC
PDB:
 4JWD
PDB:
 4JWE
PDB:
 4JWI
PDB:
 4R5G
PDB:
 4R5I
PDB:
 4R5J
PDB:
 4R5K
PDB:
 4R5L
PDB:
 5NRO
PDB:
 5OOW
PDB:
 3DPO
PDB:
 2KHO
PDB:
 2BPR
PDB:
 1Q5L
PDB:
 1DKZ
PDB:
 1DKY
PDB:
 1DKX
PDB:
 1DKG
PDB:
 1DG4
PDB:
 1BPR
PDB:
 4EZX
PFAM:
 PF00012
PRIDE:
 P0A6Y8
PRINTS:
 PR00301
PRODB:
 PRO_000022465
PROSITE:
 PS00329
PROSITE:
 PS00297
PROSITE:
 PS01036
REFSEQ:
 NP_414555
SMR:
 P0A6Y8
SWISSMODEL:
 P0A6Y8
UNIPROT:
 P0A6Y8


Operon      
Name: dnaK-tpke11-dnaJ         
Operon arrangement:
Transcription unit        Promoter
dnaKJ
dnaKJ
dnaKJ
tpke11


Regulation by small RNA    
  Display Regulation
small RNA gcvB


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter yaaWp3 11542 reverse Similarity to the consensus
Read more > 		[ICWHO] [36]
  promoter yaaIp4 11825 reverse Similarity to the consensus
Read more > 		[ICWHO] [36]
  promoter yaaIp3 11913 reverse Similarity to the consensus
Read more > 		[ICWHO] [36]
  promoter yaaIp2 11938 reverse Similarity to the consensus
Read more > 		[ICWHO] [36]
  promoter TSS_27 12142 forward nd [RS-EPT-CBR] [37]
  promoter TSS_28 12891 forward nd [RS-EPT-CBR] [37]
  promoter TSS_29 13044 forward nd [RS-EPT-CBR] [37]
  promoter TSS_30 13046 forward nd [RS-EPT-CBR] [37]
  promoter TSS_31 (cluster) 13048 forward For this promoter, there
Read more > 		[RS-EPT-CBR] [37]
  promoter TSS_32 (cluster) 13052 forward For this promoter, there
Read more > 		[RS-EPT-CBR] [37]
  promoter TSS_33 13058 forward nd [RS-EPT-CBR] [37]
  promoter TSS_34 13064 forward nd [RS-EPT-CBR] [37]
  promoter TSS_35 (cluster) 13082 forward For this promoter, there
Read more > 		[RS-EPT-CBR] [37]
  promoter TSS_36 13111 forward nd [RS-EPT-CBR] [37]
  promoter TSS_37 13127 forward nd [RS-EPT-CBR] [37]
  promoter TSS_38 13129 forward nd [RS-EPT-CBR] [37]


Evidence    

 [ICWHO] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Saito H., Uchida H., 1977, Initiation of the DNA replication of bacteriophage lambda in Escherichia coli K12., J Mol Biol 113(1):1-25

 [2] Yochem J., Uchida H., Sunshine M., Saito H., Georgopoulos CP., Feiss M., 1978, Genetic analysis of two genes, dnaJ and dnaK, necessary for Escherichia coli and bacteriophage lambda DNA replication., Mol Gen Genet 164(1):9-14

 [3] Alberts N., Mathangasinghe Y., Nillegoda NB., 2019, In Situ Monitoring of Transiently Formed Molecular Chaperone Assemblies in Bacteria, Yeast, and Human Cells., J Vis Exp (151)

 [4] Banecki B., Zylicz M., 1996, Real time kinetics of the DnaK/DnaJ/GrpE molecular chaperone machine action., J Biol Chem 271(11):6137-43

 [5] Barthel TK., Zhang J., Walker GC., 2001, ATPase-defective derivatives of Escherichia coli DnaK that behave differently with respect to ATP-induced conformational change and peptide release., J Bacteriol 183(19):5482-90

 [6] Bauer D., Meinhold S., Jakob RP., Stigler J., Merkel U., Maier T., Rief M., Zoldak G., 2018, A folding nucleus and minimal ATP binding domain of Hsp70 identified by single-molecule force spectroscopy., Proc Natl Acad Sci U S A 115(18):4666-4671

 [7] Bertelsen EB., Chang L., Gestwicki JE., Zuiderweg ER., 2009, Solution conformation of wild-type E. coli Hsp70 (DnaK) chaperone complexed with ADP and substrate., Proc Natl Acad Sci U S A 106(21):8471-6

 [8] Bukau B., Walker GC., 1990, Mutations altering heat shock specific subunit of RNA polymerase suppress major cellular defects of E. coli mutants lacking the DnaK chaperone., EMBO J 9(12):4027-36

 [9] Burkholder WF., Panagiotidis CA., Silverstein SJ., Cegielska A., Gottesman ME., Gaitanaris GA., 1994, Isolation and characterization of an Escherichia coli DnaK mutant with impaired ATPase activity., J Mol Biol 242(4):364-77

 [10] Chorev DS., Baker LA., Wu D., Beilsten-Edmands V., Rouse SL., Zeev-Ben-Mordehai T., Jiko C., Samsudin F., Gerle C., Khalid S., Stewart AG., Matthews SJ., Grunewald K., Robinson CV., 2018, Protein assemblies ejected directly from native membranes yield complexes for mass spectrometry., Science 362(6416):829-834

 [11] Desantis ME., Sweeny EA., Snead D., Leung EH., Go MS., Gupta K., Wendler P., Shorter J., 2014, Conserved distal loop residues in the Hsp104 and ClpB middle domain contact nucleotide-binding domain 2 and enable Hsp70-dependent protein disaggregation., J Biol Chem 289(2):848-67

 [12] Deuerling E., Schulze-Specking A., Tomoyasu T., Mogk A., Bukau B., 1999, Trigger factor and DnaK cooperate in folding of newly synthesized proteins., Nature 400(6745):693-6

 [13] Doyle SM., Shastry S., Kravats AN., Shih YH., Miot M., Hoskins JR., Stan G., Wickner S., 2015, Interplay between E. coli DnaK, ClpB and GrpE during protein disaggregation., J Mol Biol 427(2):312-27

 [14] Durie CL., Duran EC., Lucius AL., 2018, Escherichia coli DnaK Allosterically Modulates ClpB between High- and Low-Peptide Affinity States., Biochemistry 57(26):3665-3675

 [15] Fernandez-Higuero JA., Aguado A., Perales-Calvo J., Moro F., Muga A., 2018, Activation of the DnaK-ClpB Complex is Regulated by the Properties of the Bound Substrate., Sci Rep 8(1):5796

 [16] Georgopoulos C., Tilly K., Drahos D., Hendrix R., 1982, The B66.0 protein of Escherichia coli is the product of the dnaK+ gene., J Bacteriol 149(3):1175-7

 [17] Georgopoulos CP., Lam B., Lundquist-Heil A., Rudolph CF., Yochem J., Feiss M., 1979, Identification of the C. coli dnaK (groPC756) gene product., Mol Gen Genet 172(2):143-9

 [18] Goloubinoff P., Mogk A., Zvi AP., Tomoyasu T., Bukau B., 1999, Sequential mechanism of solubilization and refolding of stable protein aggregates by a bichaperone network., Proc Natl Acad Sci U S A 96(24):13732-7

 [19] Grudniak AM., Kurek A., Szarlak J., Wolska KI., 2011, Oleanolic and ursolic acids influence affect the expression of the cysteine regulon and the stress response in Escherichia coli., Curr Microbiol 62(4):1331-6

 [20] Kadibalban AS., Bogumil D., Landan G., Dagan T., 2016, DnaK-Dependent Accelerated Evolutionary Rate in Prokaryotes., Genome Biol Evol 8(5):1590-9

 [21] Kamath-Loeb AS., Lu CZ., Suh WC., Lonetto MA., Gross CA., 1995, Analysis of three DnaK mutant proteins suggests that progression through the ATPase cycle requires conformational changes., J Biol Chem 270(50):30051-9

 [22] Kusukawa N., Yura T., 1988, Heat shock protein GroE of Escherichia coli: key protective roles against thermal stress., Genes Dev 2(7):874-82

 [23] Lopez V., Cauvi DM., Arispe N., De Maio A., 2016, Bacterial Hsp70 (DnaK) and mammalian Hsp70 interact differently with lipid membranes., Cell Stress Chaperones 21(4):609-16

 [24] Melkina OE., Khmel IA., Plyuta VA., Koksharova OA., Zavilgelsky GB., 2017, Ketones 2-heptanone, 2-nonanone, and 2-undecanone inhibit DnaK-dependent refolding of heat-inactivated bacterial luciferases in Escherichia coli cells lacking small chaperon IbpB., Appl Microbiol Biotechnol 101(14):5765-5771

 [25] Miot M., Reidy M., Doyle SM., Hoskins JR., Johnston DM., Genest O., Vitery MC., Masison DC., Wickner S., 2011, Species-specific collaboration of heat shock proteins (Hsp) 70 and 100 in thermotolerance and protein disaggregation., Proc Natl Acad Sci U S A 108(17):6915-20

 [26] Montgomery DL., Morimoto RI., Gierasch LM., 1999, Mutations in the substrate binding domain of the Escherichia coli 70 kDa molecular chaperone, DnaK, which alter substrate affinity or interdomain coupling., J Mol Biol 286(3):915-32

 [27] Schroder H., Langer T., Hartl FU., Bukau B., 1993, DnaK, DnaJ and GrpE form a cellular chaperone machinery capable of repairing heat-induced protein damage., EMBO J 12(11):4137-44

 [28] Skowyra D., Georgopoulos C., Zylicz M., 1990, The E. coli dnaK gene product, the hsp70 homolog, can reactivate heat-inactivated RNA polymerase in an ATP hydrolysis-dependent manner., Cell 62(5):939-44

 [29] Slepenkov SV., Patchen B., Peterson KM., Witt SN., 2003, Importance of the D and E helices of the molecular chaperone DnaK for ATP binding and substrate release., Biochemistry 42(19):5867-76

 [30] Sugimoto S., Arita-Morioka KI., Terao A., Yamanaka K., Ogura T., Mizunoe Y., 2018, Multitasking of Hsp70 chaperone in the biogenesis of bacterial functional amyloids., Commun Biol 1:52

 [31] Szabo A., Langer T., Schroder H., Flanagan J., Bukau B., Hartl FU., 1994, The ATP hydrolysis-dependent reaction cycle of the Escherichia coli Hsp70 system DnaK, DnaJ, and GrpE., Proc Natl Acad Sci U S A 91(22):10345-9

 [32] Teter SA., Houry WA., Ang D., Tradler T., Rockabrand D., Fischer G., Blum P., Georgopoulos C., Hartl FU., 1999, Polypeptide flux through bacterial Hsp70: DnaK cooperates with trigger factor in chaperoning nascent chains., Cell 97(6):755-65

 [33] Tomoyasu T., Ogura T., Tatsuta T., Bukau B., 1998, Levels of DnaK and DnaJ provide tight control of heat shock gene expression and protein repair in Escherichia coli., Mol Microbiol 30(3):567-81

 [34] Wild J., Kamath-Loeb A., Ziegelhoffer E., Lonetto M., Kawasaki Y., Gross CA., 1992, Partial loss of function mutations in DnaK, the Escherichia coli homologue of the 70-kDa heat shock proteins, affect highly conserved amino acids implicated in ATP binding and hydrolysis., Proc Natl Acad Sci U S A 89(15):7139-43

 [35] Zolkiewski M., Chesnokova LS., Witt SN., 2016, Reactivation of Aggregated Proteins by the ClpB/DnaK Bi-Chaperone System., Curr Protoc Protein Sci 83:28.10.1-28.10.18

 [36] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [37] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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