RegulonDB

Gene
Name:	cbpA
Synonym(s):	ECK0991, EG12193, b1000
Genome position(nucleotides):	1062855 <-- 1063775
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.88
External database links:

ASAP:	ABE-0003379
CGSC:	31822
ECHOBASE:	EB2110
ECOLIHUB:	cbpA
OU-MICROARRAY:	b1000
STRING:	511145.b1000
COLOMBOS:	cbpA

Gene

Name:

cbpA

Synonym(s):

ECK0991, EG12193, b1000

Genome position(nucleotides):

1062855 <-- 1063775

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

52.88

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

Comment

5 -> 66

DYYAIMGVKPTDDLKTIKTAYRRLARKYHPDVSKEPDAEARFKEVAEAWEVLSDEQRRAEYD

26 -> 26

R → E: significant reduction in dimerization; unable to interact with CbpM in vivo

30 -> 30

R → E: significant reduction in dimerization and interaction with CbpM

33 -> 33

makes crucial contact with CbpM ; direct interaction with CbpM Glu-62

116 -> 116

R → A: prevents DNA binding but does not disrupt CbpA dimerization or binding to CbpM

Type

Positions

Sequence

Comment

5 -> 66

DYYAIMGVKPTDDLKTIKTAYRRLARKYHPDVSKEPDAEARFKEVAEAWEVLSDEQRRAEYD

26 -> 26

R → E: significant reduction in dimerization; unable to interact with CbpM in vivo

30 -> 30

R → E: significant reduction in dimerization and interaction with CbpM

33 -> 33

makes crucial contact with CbpM ; direct interaction with CbpM Glu-62

116 -> 116

R → A: prevents DNA binding but does not disrupt CbpA dimerization or binding to CbpM

120 -> 276

IEIEVAVFLEETLTEHKRTISYNLPVYNAFGMIEQEIPKTLNVKIPAGVGNGQRIRLKGQGTPGENGGPNGDLWLVIHIAPHPLFDIVGQDLEIVVPVSPWEAALGAKVTVPTLKESILLTIPPGSQAGQRLRVKGKGLVSKKQTGDLYAVLKIVMP

294 -> 306

QSSFDPRKDWGKA

UniProt: In Ref. 1; BAA03950..

Multifun Terms (GenProtEC)

2 - information transfer --> 2.3 - protein related --> 2.3.4 - chaperoning, repair (refolding)

2 - information transfer --> 2.3 - protein related --> 2.3.7 - nucleoproteins, basic proteins

Gene Ontology Terms (GO)

cellular_component

GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0009295 - nucleoid
GO:0043590 - bacterial nucleoid

molecular_function

GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0051082 - unfolded protein binding
GO:0003681 - bent DNA binding
GO:0042802 - identical protein binding

biological_process

GO:0006457 - protein folding
GO:0042026 - protein refolding
GO:0051085 - chaperone cofactor-dependent protein refolding

Transcriptional Regulation
	Display Regulation
Repressed by:	Fis

Transcriptional Regulation

Display Regulation

Repressed by:

Fis

	Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
	promoter	TSS_1312	1063512		reverse	nd	[RS-EPT-CBR]	[18]
	promoter	TSS_1313	1063599		reverse	nd	[RS-EPT-CBR]	[18]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_1312

1063512

reverse

[RS-EPT-CBR]

[18]

promoter

TSS_1313

1063599

reverse

[RS-EPT-CBR]

[18]

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

Evidence

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

Reference(s)
[1] Azam TA., Hiraga S., Ishihama A., 2000, Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid., Genes Cells 5(8):613-26
[2] Bird JG., Sharma S., Roshwalb SC., Hoskins JR., Wickner S., 2006, Functional analysis of CbpA, a DnaJ homolog and nucleoid-associated DNA-binding protein., J Biol Chem 281(45):34349-56
[3] Chae C., Sharma S., Hoskins JR., Wickner S., 2004, CbpA, a DnaJ homolog, is a DnaK co-chaperone, and its activity is modulated by CbpM., J Biol Chem 279(32):33147-53
[4] Chenoweth MR., Trun N., Wickner S., 2007, In vivo modulation of a DnaJ homolog, CbpA, by CbpM., J Bacteriol 189(9):3635-8
[5] Chenoweth MR., Wickner S., 2008, Complex regulation of the DnaJ homolog CbpA by the global regulators sigmaS and Lrp, by the specific inhibitor CbpM, and by the proteolytic degradation of CbpM., J Bacteriol 190(15):5153-61
[6] Chintakayala K., Grainger DC., 2011, A conserved acidic amino acid mediates the interaction between modulators and co-chaperones in enterobacteria., J Mol Biol 411(2):313-20
[7] Chintakayala K., Sellars LE., Singh SS., Shahapure R., Westerlaken I., Meyer AS., Dame RT., Grainger DC., 2015, DNA recognition by Escherichia coli CbpA protein requires a conserved arginine-minor-groove interaction., Nucleic Acids Res 43(4):2282-92
[8] Chintakayala K., Singh SS., Rossiter AE., Shahapure R., Dame RT., Grainger DC., 2013, E. coli Fis protein insulates the cbpA gene from uncontrolled transcription., PLoS Genet 9(1):e1003152
[9] Cosgriff S., Chintakayala K., Chim YT., Chen X., Allen S., Lovering AL., Grainger DC., 2010, Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA., Mol Microbiol 77(5):1289-300
[10] Gur E., Biran D., Shechter N., Genevaux P., Georgopoulos C., Ron EZ., 2004, The Escherichia coli DjlA and CbpA proteins can substitute for DnaJ in DnaK-mediated protein disaggregation., J Bacteriol 186(21):7236-42
[11] Gur E., Katz C., Ron EZ., 2005, All three J-domain proteins of the Escherichia coli DnaK chaperone machinery are DNA binding proteins., FEBS Lett 579(9):1935-9
[12] Meyer AS., Grainger DC., 2013, The Escherichia coli Nucleoid in Stationary Phase., Adv Appl Microbiol 83:69-86
[13] Sarraf NS., Baardsnes J., Cheng J., O'Connor-McCourt M., Cygler M., Ekiel I., 2010, Structural basis of the regulation of the CbpA co-chaperone by its specific modulator CbpM., J Mol Biol 398(1):111-21
[14] Sarraf NS., Shi R., McDonald L., Baardsnes J., Zhang L., Cygler M., Ekiel I., 2014, Structure of CbpA J-domain bound to the regulatory protein Cbpm explains its specificity and suggests evolutionary link between Cbpm and transcriptional regulators., PLoS One 9(6):e100441
[15] Sugimoto S., Yamanaka K., Niwa T., Terasawa Y., Kinjo Y., Mizunoe Y., Ogura T., 2020, Hierarchical Model for the Role of J-Domain Proteins in Distinct Cellular Functions., J Mol Biol 433(3):166750
[16] Ueguchi C., Kakeda M., Yamada H., Mizuno T., 1994, An analogue of the DnaJ molecular chaperone in Escherichia coli., Proc Natl Acad Sci U S A 91(3):1054-8
[17] Yamada H., Muramatsu S., Mizuno T., 1990, An Escherichia coli protein that preferentially binds to sharply curved DNA., J Biochem 108(3):420-5
[18] 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.

Reference(s)

[1] Azam TA., Hiraga S., Ishihama A., 2000, Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid., Genes Cells 5(8):613-26

[2] Bird JG., Sharma S., Roshwalb SC., Hoskins JR., Wickner S., 2006, Functional analysis of CbpA, a DnaJ homolog and nucleoid-associated DNA-binding protein., J Biol Chem 281(45):34349-56

[3] Chae C., Sharma S., Hoskins JR., Wickner S., 2004, CbpA, a DnaJ homolog, is a DnaK co-chaperone, and its activity is modulated by CbpM., J Biol Chem 279(32):33147-53

[4] Chenoweth MR., Trun N., Wickner S., 2007, In vivo modulation of a DnaJ homolog, CbpA, by CbpM., J Bacteriol 189(9):3635-8

[5] Chenoweth MR., Wickner S., 2008, Complex regulation of the DnaJ homolog CbpA by the global regulators sigmaS and Lrp, by the specific inhibitor CbpM, and by the proteolytic degradation of CbpM., J Bacteriol 190(15):5153-61

[6] Chintakayala K., Grainger DC., 2011, A conserved acidic amino acid mediates the interaction between modulators and co-chaperones in enterobacteria., J Mol Biol 411(2):313-20

[7] Chintakayala K., Sellars LE., Singh SS., Shahapure R., Westerlaken I., Meyer AS., Dame RT., Grainger DC., 2015, DNA recognition by Escherichia coli CbpA protein requires a conserved arginine-minor-groove interaction., Nucleic Acids Res 43(4):2282-92

[8] Chintakayala K., Singh SS., Rossiter AE., Shahapure R., Dame RT., Grainger DC., 2013, E. coli Fis protein insulates the cbpA gene from uncontrolled transcription., PLoS Genet 9(1):e1003152

[9] Cosgriff S., Chintakayala K., Chim YT., Chen X., Allen S., Lovering AL., Grainger DC., 2010, Dimerization and DNA-dependent aggregation of the Escherichia coli nucleoid protein and chaperone CbpA., Mol Microbiol 77(5):1289-300

[10] Gur E., Biran D., Shechter N., Genevaux P., Georgopoulos C., Ron EZ., 2004, The Escherichia coli DjlA and CbpA proteins can substitute for DnaJ in DnaK-mediated protein disaggregation., J Bacteriol 186(21):7236-42

[11] Gur E., Katz C., Ron EZ., 2005, All three J-domain proteins of the Escherichia coli DnaK chaperone machinery are DNA binding proteins., FEBS Lett 579(9):1935-9

[12] Meyer AS., Grainger DC., 2013, The Escherichia coli Nucleoid in Stationary Phase., Adv Appl Microbiol 83:69-86

[13] Sarraf NS., Baardsnes J., Cheng J., O'Connor-McCourt M., Cygler M., Ekiel I., 2010, Structural basis of the regulation of the CbpA co-chaperone by its specific modulator CbpM., J Mol Biol 398(1):111-21

[14] Sarraf NS., Shi R., McDonald L., Baardsnes J., Zhang L., Cygler M., Ekiel I., 2014, Structure of CbpA J-domain bound to the regulatory protein Cbpm explains its specificity and suggests evolutionary link between Cbpm and transcriptional regulators., PLoS One 9(6):e100441

[15] Sugimoto S., Yamanaka K., Niwa T., Terasawa Y., Kinjo Y., Mizunoe Y., Ogura T., 2020, Hierarchical Model for the Role of J-Domain Proteins in Distinct Cellular Functions., J Mol Biol 433(3):166750

[16] Ueguchi C., Kakeda M., Yamada H., Mizuno T., 1994, An analogue of the DnaJ molecular chaperone in Escherichia coli., Proc Natl Acad Sci U S A 91(3):1054-8

[17] Yamada H., Muramatsu S., Mizuno T., 1990, An Escherichia coli protein that preferentially binds to sharply curved DNA., J Biochem 108(3):420-5

[18] 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.