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Standard Name

clpB

Gene Synonym(s)

ECK2590, b2592, JW2573, htpM[1]

Product Desc.

ClpB chaperone[2][3]

ATP-dependent protease and chaperone; protein disaggregation chaperone; role in de novo protein folding under mild stress conditions[4]

Product Synonyms(s)

protein disaggregation chaperone[1], B2592[2][1], HtpM[2][1], ClpB[2][1], F84.1[2][1], F68.5[2][1], E89[2][1]

Function from GO

Cellular Component

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): clpB[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(clpB)    Textpresso(clpB)

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See Help:Quickview for help with entering information in the Quickview table.

Notes

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clpB is required for growth below 8C, which is enabled by transgenic Oleispira antarctica Cpn10/60. HT_Cmplx30_Mem: ClpB+DnaK+InfB+RpsA.[4]



Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

clpB

Mnemonic

Caseinolytic protease

Synonyms

ECK2590, b2592, JW2573, htpM[1]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

58.83 minutes 

MG1655: 2732195..2729622
gbrowse_img.php?coord=2729622..2732195&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 2655581..2653008
gbrowse_img.php?coord=2653008..2655581&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 2732829..2730256
gbrowse_img.php?coord=2730256..2732829&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 2823960..2821387
gbrowse_img.php?coord=2821387..2823960&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 2615434..2618007
gbrowse_img.php?coord=2615434..2618007&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature typeLocationDescription
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

clpBR819A

R819A

Loss of ability to form oligomers; loss of chaperone activity

seeded from UniProt:P63284

clpBE826A

E826A

No effect

seeded from UniProt:P63284

clpBGAR813AAA

GAR813AAA

No effect on oligomerization

seeded from UniProt:P63284

clpBR815A

R815A

Loss of ability to form oligomers; loss of chaperone activity

seeded from UniProt:P63284

clpBR756A

R756A

No effect on oligomerization. Loss of ATPase activity

seeded from UniProt:P63284

clpBD797A

D797A

No effect

seeded from UniProt:P63284

clpBE678A

E678A

No effect on oligomerization

seeded from UniProt:P63284

clpBK611T

K611T

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

seeded from UniProt:P63284

clpBE257A

E257A

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

seeded from UniProt:P63284

clpBE279A

E279A

No effect on oligomerization

seeded from UniProt:P63284

clpBW543F

W543F

No effect on chaperone activity or ability to form oligomers

seeded from UniProt:P63284

clpBY251A

Y251A

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

seeded from UniProt:P63284

clpBR332A

R332A

Loss of ability to form oligomers

seeded from UniProt:P63284

clpBE254A

E254A

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

seeded from UniProt:P63284

clpBK212T

K212T

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

seeded from UniProt:P63284

clpBE109A

E109A

Loss of chaperone activity

seeded from UniProt:P63284

clpBL110Q

L110Q

30% decrease in chaperone activity; retains ATPase activity

seeded from UniProt:P63284

clpBS84A

S84A

No effect

seeded from UniProt:P63284

clpBL93Q

L93Q

Loss of chaperone activity. Retains ATPase activity

seeded from UniProt:P63284

clpBL97Q

L97Q

75% decrease in chaperone activity; retains ATPase activity

seeded from UniProt:P63284

clpBD103A

D103A

Loss of chaperone activity

seeded from UniProt:P63284

clpBT7A

T7A

Loss of chaperone activity

seeded from UniProt:P63284

ΔclpB (Keio:JW2573)

deletion

deletion

PMID:16738554

Shigen

clpB102(del-ins)::kan

PMID:2066329

CGSC:90921


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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW2573

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCGTCTGGATCGTCTTACTAA

Primer 2:CCtTGGACGGCGACAATCCGGTC

nadB51::Tn10

Linked marker

CAG18480 = CGSC7419[5]

est. P1 cotransduction: 48% [6]

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[5]

est. P1 cotransduction: 77% [6]

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10157

EchoBASE (EcoliWiki Page)

EchoBASE:EB0155

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2592

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3114

EcoGene (EcoliWiki Page)

EcoGene:EG10157

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:CLPB

CGSC (EcoliWiki Page)

CGSC:32875

ASAP (EcoliWikiPage)

ASAP:ABE-0008527


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Notes

Links

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

ClpB

Synonyms

protein disaggregation chaperone[1], B2592[2][1], HtpM[2][1], ClpB[2][1], F84.1[2][1], F68.5[2][1], E89[2][1]

Product description

ClpB chaperone[2][3]

ATP-dependent protease and chaperone; protein disaggregation chaperone; role in de novo protein folding under mild stress conditions[4]

EC number (for enzymes)


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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0005524

ATP binding

GO_REF:0000002
GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR001270
InterPro:IPR003959
SP_KW:KW-0067

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0005515

protein binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004176

F

Seeded from EcoCyc [8]

complete

GO:0000166

nucleotide binding

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR003593
SP_KW:KW-0547

F

Seeded from EcoCyc [8]

complete

GO:0005737

cytoplasm

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc 12.5 [7]

complete

GO:0006950

response to stress

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0346

P

Seeded from EcoCyc [8]

complete

GO:0017111

nucleoside-triphosphatase activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc [8]

complete

GO:0019538

protein metabolic process

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004176

P

Seeded from EcoCyc [8]

complete

GO:0005624

membrane fraction

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc [8]

complete

GO:0006457

protein folding

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0005739

mitochondrion

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc [8]

complete

GO:0005829

cytosol

PMID:16858726

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc [8]

complete

GO:0009050

glycopeptide catabolic process

P

Seeded from EcoCyc 11.1[3].

required fields missing

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner TypePartnerNotesReferencesEvidence

Protein

rpsB

PMID:15690043

Experiment(s):EBI-884811

Protein

tufA

PMID:15690043

Experiment(s):EBI-884811

Protein

ydeP

PMID:15690043

Experiment(s):EBI-891673

Protein

ccmB

PMID:15690043

Experiment(s):EBI-891673

Protein

rnz

PMID:15690043

Experiment(s):EBI-891673

Protein

glcB

PMID:15690043

Experiment(s):EBI-891673

Protein

lasT

PMID:15690043

Experiment(s):EBI-891673

Protein

ptsN

PMID:15690043

Experiment(s):EBI-891673

Protein

rplC

PMID:15690043

Experiment(s):EBI-891673

Protein

rplM

PMID:15690043

Experiment(s):EBI-891673

Protein

rplU

PMID:15690043

Experiment(s):EBI-891673

Protein

rplV

PMID:15690043

Experiment(s):EBI-891673

Protein

rpmC

PMID:15690043

Experiment(s):EBI-891673

Protein

rpsG

PMID:15690043

Experiment(s):EBI-891673

Protein

rpsH

PMID:15690043

Experiment(s):EBI-891673

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-891673

Protein

rpsN

PMID:15690043

Experiment(s):EBI-891673

Protein

sapC

PMID:15690043

Experiment(s):EBI-891673

Protein

thiG

PMID:15690043

Experiment(s):EBI-891673

Protein

yagW

PMID:15690043

Experiment(s):EBI-891673

Protein

ygaU

PMID:15690043

Experiment(s):EBI-891673

Protein

yhfT

PMID:15690043

Experiment(s):EBI-891673

Protein

gfcB

PMID:15690043

Experiment(s):EBI-891673

Protein

evgS

PMID:15690043

Experiment(s):EBI-891673

Protein

putA

PMID:16606699

Experiment(s):EBI-1143404

Protein

uidC

PMID:16606699

Experiment(s):EBI-1143404

Protein

lacZ

PMID:16606699

Experiment(s):EBI-1143404

Protein

ptsP

PMID:16606699

Experiment(s):EBI-1143404

Protein

yjbH

PMID:16606699

Experiment(s):EBI-1143404

Protein

alaS

PMID:16606699

Experiment(s):EBI-1143404

Protein

ulaF

PMID:16606699

Experiment(s):EBI-1143404

Protein

phoB

PMID:16606699

Experiment(s):EBI-1143404

Protein

rplB

PMID:16606699

Experiment(s):EBI-1143404

Protein

sdhA

PMID:16606699

Experiment(s):EBI-1143404

Protein

nadE

PMID:16606699

Experiment(s):EBI-1143404

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

CompartmentDescriptionEvidenceSourceNotes

cytoplasm


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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Sequence

at EcoCyc 

MRLDRLTNKF QLALADAQSL ALGHDNQFIE PLHLMSALLN QEGGSVSPLL TSAGINAGQL
RTDINQALNR LPQVEGTGGD VQPSQDLVRV LNLCDKLAQK RGDNFISSEL FVLAALESRG
TLADILKAAG ATTANITQAI EQMRGGESVN DQGAEDQRQA LKKYTIDLTE RAEQGKLDPV
IGRDEEIRRT IQVLQRRTKN NPVLIGEPGV GKTAIVEGLA QRIINGEVPE GLKGRRVLAL
DMGALVAGAK YRGEFEERLK GVLNDLAKQE GNVILFIDEL HTMVGAGKAD GAMDAGNMLK
PALARGELHC VGATTLDEYR QYIEKDAALE RRFQKVFVAE PSVEDTIAIL RGLKERYELH
HHVQITDPAI VAAATLSHRY IADRQLPDKA IDLIDEAASS IRMQIDSKPE ELDRLDRRII
QLKLEQQALM KESDEASKKR LDMLNEELSD KERQYSELEE EWKAEKASLS GTQTIKAELE
QAKIAIEQAR RVGDLARMSE LQYGKIPELE KQLEAATQLE GKTMRLLRNK VTDAEIAEVL
ARWTGIPVSR MMESEREKLL RMEQELHHRV IGQNEAVDAV SNAIRRSRAG LADPNRPIGS
FLFLGPTGVG KTELCKALAN FMFDSDEAMV RIDMSEFMEK HSVSRLVGAP PGYVGYEEGG
YLTEAVRRRP YSVILLDEVE KAHPDVFNIL LQVLDDGRLT DGQGRTVDFR NTVVIMTSNL
GSDLIQERFG ELDYAHMKEL VLGVVSHNFR PEFINRIDEV VVFHPLGEQH IASIAQIQLK
RLYKRLEERG YEIHISDEAL KLLSENGYDP VYGARPLKRA IQQQIENPLA QQILSGELVP
GKVIRLEVNE DRIVAVQ
Length

857

Mol. Wt

95.587 kDa

pI

5.3 (calculated)

Extinction coefficient

36,330 - 36,705 (calc based on 17 Y, 2 W, and 3 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

TypeResiduesDescriptionNotesReferences
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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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Resource typeSourceNotes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10157-MONOMER

UniProt (EcoliWiki Page)

UniProt:P63284

PFAM (EcoliWiki Page)

PFAM:PF02861

RefSeq (EcoliWiki Page)

RefSeq:NP_417083


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Notes

Links

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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

clpB

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Figure courtesy of RegulonDB

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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gbrowse_img.php?coord=2732175..2732215&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

microarray

GEO Profiles:b2592 (EcoliWiki Page)

NCBI GEO profiles for clpB

microarray

GenExpDB:b2592 (EcoliWiki Page)

Summary of data for clpB from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource NameResource TypeDescriptionSourceNotes

GFP Fusion

Intergenic region (2732124..2732340) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ04; Well:D12[9]

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Notes

Accessions Related to clpB Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10157

EchoBASE (EcoliWiki Page)

EchoBASE:EB0155

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2592

EcoGene (EcoliWiki Page)

EcoGene:EG10157


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Notes

Links

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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

OrganismHomologs (Statistics)Comments

Anopheles gambiae

  • ENSANGP00000013686 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT5G15450 (score: 1.000; bootstrap: 85%)
  • AT2G25140 (score: 0.355)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000001687 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000008558 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0231601 (score: 1.000; bootstrap: 62%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000294053 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000007168 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000009875 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q75GT3 (score: 1.000; bootstrap: 87%)
  • Q75I57 (score: 0.525)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000006940 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000026665 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YDR258C (score: 1.000; bootstrap: 84%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPBC16D108c (score: 1.000; bootstrap: 57%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000137929 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00038721001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000022882 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

CLPB

From SHIGELLACYC

E. coli O157

CLPB

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF02861


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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 2.13 2.14 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
  7. ↑ 7.0 7.1 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 8.6 8.7 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  9. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

Categories

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