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Standard Name

clpX

Gene Synonym(s)

ECK0432, b0438, JW0428, LopC[1]

Product Desc.

ClpX[2][3];

Component of ClpX ATP-dependent protease specificity component and chaperone[3]; ClpAXP[3]; ClpXP[3]

ATPase subunit of ClpXP protease; ClpXP degrades ssrA-tagged proteins; molecular chaperone[4]

Product Synonyms(s)

ATPase and specificity subunit of ClpX-ClpP ATP-dependent serine protease[1], B0438[2][1], LopC[2][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

transcription unit(s): clpPX[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(clpX)    Textpresso(clpX)

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Notes

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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

clpX

Mnemonic

Caseinolytic protease

Synonyms

ECK0432, b0438, JW0428, LopC[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

9.84 minutes 

MG1655: 456650..457924
gbrowse_img.php?coord=456650..457924&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 428131..429405
gbrowse_img.php?coord=428131..429405&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 456650..457924
gbrowse_img.php?coord=456650..457924&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 395981..397255
gbrowse_img.php?coord=395981..397255&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 359409..360683
gbrowse_img.php?coord=359409..360683&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

ΔclpX (Keio:JW0428)

deletion

deletion

PMID:16738554

Shigen
CGSC8591[5]

clpX

PMID:12519969

ASAP

At position 641 in Plus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20174

E185Q

E185Q

Other

Loss of ATP hydrolysis in vitro

PMID:15989952

Mutant protein retains normal assembly, ATP binding , and the ability to bind polypeptide substrates

clpX103(del-ins)::kan

PMID:8226770

CGSC:90914

ΔclpX724::kan

PMID:16738554

CGSC:100344


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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

JW0428

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACAGATAAACGCAAAGATGG

Primer 2:CCTTCACCAGATGCCTGTTGCGC

tsx-247::Tn10

Linked marker

CAG12148 = CGSC7337[5]

est. P1 cotransduction: 39% [6]

zaj-3054::Tn10

Linked marker

CAG12017 = CGSC7339[5]

est. P1 cotransduction: 92% [6]
Synonyms:zba-3054::Tn10

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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:EG10159

EchoBASE (EcoliWiki Page)

EchoBASE:EB0157

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0438

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0554

EcoGene (EcoliWiki Page)

EcoGene:EG10159

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:CLPX

CGSC (EcoliWiki Page)

CGSC:31287

ASAP (EcoliWikiPage)

ASAP:ABE-0001517


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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

ClpX

Synonyms

ATPase and specificity subunit of ClpX-ClpP ATP-dependent serine protease[1], B0438[2][1], LopC[2][1]

Product description

ClpX[2][3];

Component of ClpX ATP-dependent protease specificity component and chaperone[3]; ClpAXP[3]; ClpXP[3]

ATPase subunit of ClpXP protease; ClpXP degrades ssrA-tagged proteins; molecular chaperone[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:0046872

metal ion binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc [7]

complete

GO:0019538

protein metabolic process

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010603

P

Seeded from EcoCyc [7]

complete

GO:0017111

nucleoside-triphosphatase activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc [7]

complete

GO:0015031

protein transport

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004487

P

Seeded from EcoCyc [7]

complete

GO:0016887

ATPase activity

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004487
InterPro:IPR010603

F

Seeded from EcoCyc [7]

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 [7]

complete

GO:0005515

protein binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004487

F

Seeded from EcoCyc [7]

complete

GO:0005524

ATP binding

GO_REF:0000002
GO_REF:0000004
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR004487
SP_KW:KW-0067
HAMAP:MF_00175

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0006457

protein folding

GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00175

P

Seeded from EcoCyc [7]

complete

GO:0006950

response to stress

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0346

P

Seeded from EcoCyc [7]

complete

GO:0008270

zinc ion binding

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR010603
SP_KW:KW-0862

F

Seeded from EcoCyc [7]

complete

GO:0046983

protein dimerization activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010603

F

Seeded from EcoCyc [7]

complete

GO:0051082

unfolded protein binding

GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00175

F

Seeded from EcoCyc [7]

complete

GO:0009050

glycopeptide catabolic process

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0006508

proteolysis

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0005737

cytoplasm

C

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

Subunits of ClpX ATP-dependent protease specificity component and chaperone

could be indirect

Protein

clpA

PMID:15690043

Experiment(s):EBI-884518

Protein

clpB

PMID:15690043

Experiment(s):EBI-884518

Protein

metK

PMID:15690043

Experiment(s):EBI-884518

Protein

mreB

PMID:15690043

Experiment(s):EBI-884518

Protein

pstB

PMID:15690043

Experiment(s):EBI-884518

Protein

tufA

PMID:15690043

Experiment(s):EBI-884518

Protein

hscB

PMID:15690043

Experiment(s):EBI-884518

Protein

ahpC

PMID:15690043

Experiment(s):EBI-891405

Protein

dnaK

PMID:15690043

Experiment(s):EBI-891405

Protein

grpE

PMID:15690043

Experiment(s):EBI-891405

Protein

rfbB

PMID:15690043

Experiment(s):EBI-891405

Protein

rplL

PMID:15690043

Experiment(s):EBI-891405

Protein

rpmC

PMID:15690043

Experiment(s):EBI-891405

Protein

rpmG

PMID:15690043

Experiment(s):EBI-891405

Protein

slyB

PMID:16606699

Experiment(s):EBI-1136646

Protein

intD

PMID:16606699

Experiment(s):EBI-1136646

Protein

hypB

PMID:16606699

Experiment(s):EBI-1136646

Protein

rho

PMID:16606699

Experiment(s):EBI-1136646

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1136646

Protein

inaA

PMID:16606699

Experiment(s):EBI-1136646

Protein

yhbJ

PMID:16606699

Experiment(s):EBI-1136646

Protein

yibL

PMID:16606699

Experiment(s):EBI-1136646

Protein

ybhK

PMID:16606699

Experiment(s):EBI-1136646

Protein

sdhA

PMID:16606699

Experiment(s):EBI-1136646

Protein

nadE

PMID:16606699

Experiment(s):EBI-1136646

Protein

Subunits of ClpAXP

could be indirect

Protein

Subunits of ClpXP

could be indirect


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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes
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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 

MTDKRKDGSG KLLYCSFCGK SQHEVRKLIA GPSVYICDEC VDLCNDIIRE EIKEVAPHRE
RSALPTPHEI RNHLDDYVIG QEQAKKVLAV AVYNHYKRLR NGDTSNGVEL GKSNILLIGP
TGSGKTLLAE TLARLLDVPF TMADATTLTE AGYVGEDVEN IIQKLLQKCD YDVQKAQRGI
VYIDEIDKIS RKSDNPSITR DVSGEGVQQA LLKLIEGTVA AVPPQGGRKH PQQEFLQVDT
SKILFICGGA FAGLDKVISH RVETGSGIGF GATVKAKSDK ASEGELLAQV EPEDLIKFGL
IPEFIGRLPV VATLNELSEE ALIQILKEPK NALTKQYQAL FNLEGVDLEF RDEALDAIAK
KAMARKTGAR GLRSIVEAAL LDTMYDLPSM EDVEKVVIDE SVIDGQSKPL LIYGKPEAQQ ASGE
Length

424

Mol. Wt

46.356 kDa

pI

5.1 (calculated)

Extinction coefficient

16,390 - 17,265 (calc based on 11 Y, W, and 7 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

Initiator Methionine

1

Removed

UniProt:P0A6H1


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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:EG10159-MONOMER

SwissModel (EcoliWiki Page)

SwissModel:P0A6H1

UniProt (EcoliWiki Page)

UniProt:P0A6H1

PFAM (EcoliWiki Page)

PFAM:PF06689

RefSeq (EcoliWiki Page)

RefSeq:NP_414972


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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)

clpPX

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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=456630..456670&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein&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:b0438 (EcoliWiki Page)

NCBI GEO profiles for clpX

microarray

GenExpDB:b0438 (EcoliWiki Page)

Summary of data for clpX 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 (456434..456661) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ20; Well:A8[9]

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Notes

Accessions Related to clpX Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10159

EchoBASE (EcoliWiki Page)

EchoBASE:EB0157

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0438

EcoGene (EcoliWiki Page)

EcoGene:EG10159


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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

  • ENSANGP00000028289 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000031124 (score: 1.000; bootstrap: 96%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT5G53350 (score: 1.000; bootstrap: 100%)
  • AT1G33360 (score: 0.317)
  • AT5G49840 (score: 0.220)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000011038 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00032922 (score: 1.000; bootstrap: 100%)
  • WBGene00026894 (score: 0.101)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00008412 (score: 1.000; bootstrap: 100%)
  • WBGene00019461 (score: 0.107)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000025235 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000011306 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-040912-143 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040912-145 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0038745 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA18242-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000011790 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000300107 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000008831 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000012965 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:1346017 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q5N8G6 (score: 1.000; bootstrap: 100%)
  • Q6Z7F0 (score: 0.408)
  • Q6KAC2 (score: 0.332)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000012262 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000050010 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YBR227C (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000132380 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00025589001 (score: 1.000; bootstrap: 100%)
  • GSTENP00003285001 (score: 0.186)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000036073 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

CLPX

From SHIGELLACYC

E. coli O157

CLPX

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF06689


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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. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.00 3.01 3.02 3.03 3.04 3.05 3.06 3.07 3.08 3.09 3.10 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 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 5.2 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. ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 7.11 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  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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