cspE:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

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

Standard name

CspE

Synonyms

DNA-binding transcriptional repressor[1], B0623[2][1], MsmC[2][1], GicA[2][1], CspE[2][1] , ECK0616, gicA, JW0618, msmC, b0623

Product description

cold shock protein CspE[2]; transcription antiterminator and regulator of RNA stability[3]

Binds and melts RNA, involved in cold acclimation; binds ssDNA; high copy protects the chromosome from decondensation by camphor and increases DNA supercoiling; dimeric[4]

EC number (for enzymes)


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Notes

Function

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

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002059

P

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

PMID:10476034[5]

IDA: Inferred from Direct Assay

F

Figure 2

complete

GO:0003697

single-stranded DNA binding

PMID:17088256[6]

IDA: Inferred from Direct Assay

F

Figure 1

complete

GO:0001072

RNA binding transcription antitermination factor activity

PMID:10884409[7]

IDA: Inferred from Direct Assay

F

Figure 1, data not shown to determine RNA interaction (HPLC size-exclusion chromatography, native PAGE, and Ni2+-nitrilotriacetic acid agarose coimmobilization assays)

complete

GO:0060567

negative regulation of transcription termination

PMID:10884409[7]

IDA: Inferred from Direct Assay

P

complete

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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 Type Partner Notes References Evidence

Protein

dnaN

PMID:15690043[8]

Experiment(s):EBI-879589

Protein

gabT

PMID:15690043[8]

Experiment(s):EBI-879589

Protein

hflB

PMID:15690043[8]

Experiment(s):EBI-879589

Protein

hrpA

PMID:15690043[8]

Experiment(s):EBI-879589

Protein

pnp

PMID:15690043[8]

Experiment(s):EBI-879589

Protein

rho

PMID:15690043[8]

Experiment(s):EBI-879589

Protein

rplA

PMID:15690043[8]

Experiment(s):EBI-879589, EBI-883848

Protein

rplB

PMID:15690043[8]

Experiment(s):EBI-879589

Protein

rplC

PMID:15690043[8]

Experiment(s):EBI-879589, EBI-883848

Protein

rpsA

PMID:15690043[8]

Experiment(s):EBI-879589

Protein

rpsD

PMID:15690043[8]

Experiment(s):EBI-879589

Protein

rpsG

PMID:15690043[8]

Experiment(s):EBI-879589, EBI-883848

Protein

secA

PMID:15690043[8]

Experiment(s):EBI-879589

Protein

rnr

PMID:15690043[8]

Experiment(s):EBI-879589

Protein

ycbY

PMID:15690043[8]

Experiment(s):EBI-879589

Protein

rluB

PMID:15690043[8]

Experiment(s):EBI-879589

Protein

dcuR

PMID:15690043[8]

Experiment(s):EBI-879589

Protein

cspI

PMID:15690043[8]

Experiment(s):EBI-883848

Protein

glmU

PMID:15690043[8]

Experiment(s):EBI-883848

Protein

hfq

PMID:15690043[8]

Experiment(s):EBI-883848

Protein

hupA

PMID:15690043[8]

Experiment(s):EBI-883848

Protein

hyfG

PMID:15690043[8]

Experiment(s):EBI-883848

Protein

rplD

PMID:15690043[8]

Experiment(s):EBI-883848

Protein

rplS

PMID:15690043[8]

Experiment(s):EBI-883848

Protein

rplX

PMID:15690043[8]

Experiment(s):EBI-883848

Protein

rpsE

PMID:15690043[8]

Experiment(s):EBI-883848

Protein

rpsJ

PMID:15690043[8]

Experiment(s):EBI-883848

Protein

rpsP

PMID:15690043[8]

Experiment(s):EBI-883848

Protein

serS

PMID:15690043[8]

Experiment(s):EBI-883848

Protein

rplB

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

rpsG

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

rpoC

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

rpsI

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

ogrK

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

rplO

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

rplD

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

ygbA

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

yafO

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

rpoB

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

hchA

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

rplA

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

uspG

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

torA

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

prs

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

rplU

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

ulaF

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

rpsD

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

nrdI

PMID:16606699[9]

Experiment(s):EBI-1137461

Protein

dnaN

PMID:19402753[10]

MALDI(Z-score):38.397986

Protein

rho

PMID:19402753[10]

MALDI(Z-score):38.327248

Protein

rpsP

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

rpsJ

PMID:19402753[10]

LCMS(ID Probability):99.0 MALDI(Z-score):3.633502

Protein

hupA

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

clpA

PMID:19402753[10]

MALDI(Z-score):21.714935

Protein

rpsA

PMID:19402753[10]

MALDI(Z-score):26.544566

Protein

rplB

PMID:19402753[10]

MALDI(Z-score):21.191895

Protein

rpsD

PMID:19402753[10]

MALDI(Z-score):35.999379

Protein

rplA

PMID:19402753[10]

LCMS(ID Probability):99.0 MALDI(Z-score):24.553794

Protein

pnp

PMID:19402753[10]

MALDI(Z-score):26.191468

Protein

hrpA

PMID:19402753[10]

MALDI(Z-score):18.161567

Protein

glmU

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

rnr

PMID:19402753[10]

MALDI(Z-score):25.704700

Protein

dcuR

PMID:19402753[10]

MALDI(Z-score):17.053160

Protein

rplD

PMID:19402753[10]

LCMS(ID Probability):99.6 MALDI(Z-score):4.393096

Protein

cspI

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

deaD

PMID:19402753[10]

MALDI(Z-score):27.600158

Protein

hfq

PMID:19402753[10]

LCMS(ID Probability):99.6

Protein

rluB

PMID:19402753[10]

LCMS(ID Probability):90.0 MALDI(Z-score):33.056271

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Notes

selective RNA binding sequence

AAAUUU

PMID: 10476034

Figure 1

Localization

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

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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

Name
Sequence

at EcoCyc 

MSKIKGNVKW FNESKGFGFI TPEDGSKDVF VHFSAIQTNG FKTLAEGQRV EFEITNGAKG
PSAANVIAL
Length

69

Mol. Wt

7.463 kDa

pI

9.6 (calculated)

Extinction coefficient

5,500 (calc based on 0 Y, 1 W, and 0 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.

Type Residues Description Notes References

Initiator Methionine

1

Removed

UniProt:P0A972

Domain

3..69

PF00313 'Cold-shock' DNA-binding domain

PMID:19920124[11]

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<motif_map/>

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

Structures

<beststructure> gene=cspE taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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

Resource type Source Notes/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.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16128606

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947024

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002142

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A972

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12179

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12179

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947024

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002072

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2096

Escherichia coli str. K-12 substr. MG1655

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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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ Phadtare, S & Inouye, M (1999) Sequence-selective interactions with RNA by CspB, CspC and CspE, members of the CspA family of Escherichia coli. Mol. Microbiol. 33 1004-14 PubMed
  6. ↑ Johnston, D et al. (2006) Specificity of DNA binding and dimerization by CspE from Escherichia coli. J. Biol. Chem. 281 40208-15 PubMed
  7. ↑ 7.0 7.1 Bae, W et al. (2000) Escherichia coli CspA-family RNA chaperones are transcription antiterminators. Proc. Natl. Acad. Sci. U.S.A. 97 7784-9 PubMed
  8. ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 8.12 8.13 8.14 8.15 8.16 8.17 8.18 8.19 8.20 8.21 8.22 8.23 8.24 8.25 8.26 8.27 8.28 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  9. ↑ 9.00 9.01 9.02 9.03 9.04 9.05 9.06 9.07 9.08 9.09 9.10 9.11 9.12 9.13 9.14 9.15 9.16 9.17 9.18 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  10. ↑ 10.00 10.01 10.02 10.03 10.04 10.05 10.06 10.07 10.08 10.09 10.10 10.11 10.12 10.13 10.14 10.15 10.16 10.17 10.18 10.19 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  11. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

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