RegulonDB

Gene
Name:	clpB
Synonym(s):	ECK2590, EG10157, b2592, htpM
Genome position(nucleotides):	2731600 <-- 2734173
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	51.44
Reference(s):	[1] Park SK., et al., 1993
External database links:

ASAP:	ABE-0008527
CGSC:	32875
ECHOBASE:	EB0155
ECOLIHUB:	clpB
MIM:	616271
OU-MICROARRAY:	b2592
STRING:	511145.b2592
COLOMBOS:	clpB

Gene

Name:

clpB

Synonym(s):

ECK2590, EG10157, b2592, htpM

Genome position(nucleotides):

2731600 <-- 2734173

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

51.44

Reference(s):

[1] Park SK., et al., 1993

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

MIM:

OU-MICROARRAY:

STRING:

COLOMBOS:

Shine dalgarno
Sequence:	gatccgttatGGGAGGagtTAT

Shine dalgarno

Sequence:

gatccgttatGGGAGGagtTAT

Type

Positions

Sequence

Comment

1 -> 148

MRLDRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDINQALNRLPQVEGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRGTLADILKAAGATTANITQAIEQMRGGES

UniProt: In isoform ClpB-3..

3 -> 146

LDRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDINQALNRLPQVEGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRGTLADILKAAGATTANITQAIEQMRGG

UniProt: Clp R.

6 -> 71

LTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDINQALNRL

UniProt: Repeat 1; Sequence Annotation Type: region of interest.

7 -> 7

UniProt: Loss of chaperone activity..

17 -> 68

AQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDINQAL

Type

Positions

Sequence

Comment

1 -> 148

MRLDRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDINQALNRLPQVEGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRGTLADILKAAGATTANITQAIEQMRGGES

UniProt: In isoform ClpB-3..

3 -> 146

LDRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDINQALNRLPQVEGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRGTLADILKAAGATTANITQAIEQMRGG

UniProt: Clp R.

6 -> 71

LTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDINQALNRL

UniProt: Repeat 1; Sequence Annotation Type: region of interest.

7 -> 7

UniProt: Loss of chaperone activity..

17 -> 68

AQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDINQAL

83 -> 146

PSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRGTLADILKAAGATTANITQAIEQMRGG

UniProt: Repeat 2; Sequence Annotation Type: region of interest.

84 -> 84

UniProt: No effect..

93 -> 93

UniProt: Loss of chaperone activity. Retains ATPase activity..

94 -> 145

CDKLAQKRGDNFISSELFVLAALESRGTLADILKAAGATTANITQAIEQMRG

96 -> 97

UniProt: In Ref. 1; AAA24422..

97 -> 97

UniProt: 75% decrease in chaperone activity; retains ATPase activity..

103 -> 103

UniProt: Loss of chaperone activity..

109 -> 109

UniProt: Loss of chaperone activity..

110 -> 110

UniProt: 30% decrease in chaperone activity; retains ATPase activity..

122 -> 122

UniProt: In Ref. 1; AAA24422..

149 -> 149

UniProt: In isoform ClpB-3..

159 -> 340

QALKKYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAE

UniProt: NBD1; Sequence Annotation Type: region of interest.

203 -> 337

VLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQKVF

206 -> 213

GEPGVGKT

UniProt: ATP 1.

212 -> 212

UniProt: Loss of ability to form oligomers even in the presence of ATP. Loss of chaperone activity..

248 -> 257

GAKYRGEFEE

potential substrate binding site located at the central pore of the first AAA domain

251 -> 251

UniProt: Decrease in ability to disaggregate proteins due to decreased substrate-binding activity. Retains hexameric quaternary structure and ATPase activity..

254 -> 254

UniProt: Decrease in ability to disaggregate proteins due to decreased substrate-binding activity. Retains hexameric quaternary structure and ATPase activity; when associated with A-257..

257 -> 257

UniProt: Decrease in ability to disaggregate proteins due to decreased substrate-binding activity. Retains hexameric quaternary structure and ATPase activity; when associated with A-254..

276 -> 279

FIDE

279 -> 279

UniProt: No effect on oligomerization..

332 -> 332

UniProt: Loss of ability to form oligomers..

341 -> 545

PSVEDTIAILRGLKERYELHHHVQITDPAIVAAATLSHRYIADRQLPDKAIDLIDEAASSIRMQIDSKPEELDRLDRRIIQLKLEQQALMKESDEASKKRLDMLNEELSDKERQYSELEEEWKAEKASLSGTQTIKAELEQAKIAIEQARRVGDLARMSELQYGKIPELEKQLEAATQLEGKTMRLLRNKVTDAEIAEVLARWTG

UniProt: Linker; Sequence Annotation Type: region of interest.

342 -> 443

SVEDTIAILRGLKERYELHHHVQITDPAIVAAATLSHRYIADRQLPDKAIDLIDEAASSIRMQIDSKPEELDRLDRRIIQLKLEQQALMKESDEASKKRLDM

409 -> 525

PEELDRLDRRIIQLKLEQQALMKESDEASKKRLDMLNEELSDKERQYSELEEEWKAEKASLSGTQTIKAELEQAKIAIEQARRVGDLARMSELQYGKIPELEKQLEAATQLEGKTMR

Middle domain

410 -> 455

EELDRLDRRIIQLKLEQQALMKESDEASKKRLDMLNEELSDKERQY

425 -> 425

alternate sequence E → A: increase in DnaK dependent disaggregation activity (gain of function mutation)

432 -> 432

alternate sequence E → A: loss of DnaK dependent disaggregation activity (loss of function mutation); normal oligomerization; no effect on substrate induced ATPase activity; mutant trapped in repressed state

456 -> 520

SELEEEWKAEKASLSGTQTIKAELEQAKIAIEQARRVGDLARMSELQYGKIPELEKQLEAATQLE

476 -> 476

alternate sequence K → C: increase in DnaK dependent disaggregation activity (gain of function mutation); increase in substrate (casein) induced ATPase activity; mutant trapped in derepressed state

480 -> 480

alternate sequence E → C: loss of DnaK dependent disaggregation activity (loss of function mutation), normal oligomerization; no effect on substrate induced ATPase activity; mutant trapped in repressed state

495 -> 503

LARMSELQY

helix 3 of the M domain interacts with the first ATPase domain (AAA1)

499 -> 499

alternate sequence S → D: defective in disaggregation activity; translocation competent (ie. retains 'threading' activity); increased basal ATPase rate and hyperstimulation of substrate (casein) induced ATPase activity

503 -> 503

alternate sequence Y → D: defective in disaggregation activity; translocation competent (ie. retains 'threading' activity); increased basal ATPase rate and hyperstimulation of substrate (casein) induced ATPase activity

530 -> 758

KVTDAEIAEVLARWTGIPVSRMMESEREKLLRMEQELHHRVIGQNEAVDAVSNAIRRSRAGLADPNRPIGSFLFLGPTGVGKTELCKALANFMFDSDEAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKAHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQERFGELDYAHMKELVLGVVSHNFRPEFINRID

543 -> 543

UniProt: No effect on chaperone activity or ability to form oligomers..

555 -> 765

EREKLLRMEQELHHRVIGQNEAVDAVSNAIRRSRAGLADPNRPIGSFLFLGPTGVGKTELCKALANFMFDSDEAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKAHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQERFGELDYAHMKELVLGVVSHNFRPEFINRIDEVVVFHP

UniProt: NBD2; Sequence Annotation Type: region of interest.

596 -> 760

RPIGSFLFLGPTGVGKTELCKALANFMFDSDEAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKAHPDVFNILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQERFGELDYAHMKELVLGVVSHNFRPEFINRIDEV

605 -> 612

GPTGVGKT

UniProt: ATP 2. Walker A motif within NBD-2

611 -> 611

UniProt: No effect on ability to form oligomers. Loss of chaperone activity..

653 -> 653

alternate seqence Y → A: mutation results in loss of substrate translocation through the central pore of the ClpB oligomer in vitro

675 -> 678

LLDE

678 -> 678

UniProt: No effect on oligomerization..

756 -> 756

UniProt: No effect on oligomerization. Loss of ATPase activity..

766 -> 857

LGEQHIASIAQIQLKRLYKRLEERGYEIHISDEALKLLSENGYDPVYGARPLKRAIQQQIENPLAQQILSGELVPGKVIRLEVNEDRIVAVQ

UniProt: C-terminal; Sequence Annotation Type: region of interest.

770 -> 857

HIASIAQIQLKRLYKRLEERGYEIHISDEALKLLSENGYDPVYGARPLKRAIQQQIENPLAQQILSGELVPGKVIRLEVNEDRIVAVQ

797 -> 797

UniProt: No effect..

813 -> 815

GAR

UniProt: No effect on oligomerization..

815 -> 815

UniProt: Loss of ability to form oligomers; loss of chaperone activity..

819 -> 819

UniProt: Loss of ability to form oligomers; loss of chaperone activity..

826 -> 826

UniProt: No effect..

55 -> 189

INAGQLRTDINQALNRLPQVEGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRGTLADILKAAGATTANITQAIEQMRGGESVNDQGAEDQRQALKKYTIDLTERAEQGKLDPVIGRDEEIRR

194 -> 295

LQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDA

448 -> 612

LSDKERQYSELEEEWKAEKASLSGTQTIKAELEQAKIAIEQARRVGDLARMSELQYGKIPELEKQLEAATQLEGKTMRLLRNKVTDAEIAEVLARWTGIPVSRMMESEREKLLRMEQELHHRVIGQNEAVDAVSNAIRRSRAGLADPNRPIGSFLFLGPTGVGKT

618 -> 697

LANFMFDSDEAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKAHPDVFNILLQVLDDG

Multifun Terms (GenProtEC)

5 - cell processes --> 5.5 - adaptations --> 5.5.2 - temperature extremes

Gene Ontology Terms (GO)

cellular_component

GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0016020 - membrane

molecular_function

GO:0005515 - protein binding
GO:0016887 - ATP hydrolysis activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0042802 - identical protein binding

biological_process

GO:0009408 - response to heat
GO:0042026 - protein refolding
GO:0034605 - cellular response to heat

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_2902	2731272	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_2903 (cluster)	2733127	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_2904 (cluster)	2734197	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_2905	2734202	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_2907	2734207	reverse	nd	[RS-EPT-CBR]	[2]
promoter	TSS_2908 (cluster)	2734293	reverse	nd	[RS-EPT-CBR]	[2]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_2902

2731272

reverse

[RS-EPT-CBR]

[2]

promoter

TSS_2903 (cluster)

2733127

reverse

[RS-EPT-CBR]

[2]

promoter

TSS_2904 (cluster)

2734197

reverse

[RS-EPT-CBR]

[2]

promoter

TSS_2905

2734202

reverse

[RS-EPT-CBR]

[2]

promoter

TSS_2907

2734207

reverse

[RS-EPT-CBR]

[2]

promoter

TSS_2908 (cluster)

2734293

reverse

[RS-EPT-CBR]

[2]

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] Park SK., Kim KI., Woo KM., Seol JH., Tanaka K., Ichihara A., Ha DB., Chung CH., 1993, Site-directed mutagenesis of the dual translational initiation sites of the clpB gene of Escherichia coli and characterization of its gene products., J Biol Chem 268(27):20170-4
[2] 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] Park SK., Kim KI., Woo KM., Seol JH., Tanaka K., Ichihara A., Ha DB., Chung CH., 1993, Site-directed mutagenesis of the dual translational initiation sites of the clpB gene of Escherichia coli and characterization of its gene products., J Biol Chem 268(27):20170-4

[2] 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.