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Protein

Cold shock-like protein CspD

Gene

cspD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Inhibits DNA replication at both initiation and elongation steps, most probably by binding to the opened, single-stranded regions at replication forks. Plays a regulatory role in chromosomal replication in nutrient-depleted cells.
Involved in persister cell formation, acting downstream of mRNA interferase (toxin) MqsR. Overproduction is toxic.

GO - Molecular functioni

  1. RNA binding Source: EcoCyc
  2. single-stranded DNA binding Source: EcoCyc

GO - Biological processi

  1. negative regulation of DNA replication Source: EcoCyc
  2. regulation of transcription, DNA-templated Source: InterPro
  3. response to starvation Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

DNA replication inhibitor, Toxin

Keywords - Ligandi

DNA-binding, RNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11111-MONOMER.
ECOL316407:JW0864-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Cold shock-like protein CspD
Short name:
CSP-D
Gene namesi
Name:cspD
Synonyms:cspH, ybjA
Ordered Locus Names:b0880, JW0864
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11111. cspD.

Subcellular locationi

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Deletion represses the production of persister cells.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 7474Cold shock-like protein CspDPRO_0000100248Add
BLAST

Proteomic databases

PaxDbiP0A968.
PRIDEiP0A968.

Expressioni

Inductioni

Not induced by cold-shock. Stationary-phase and starvation inducible, as well as by oxidative stress (30 mM H2O2). Repressed by MqsA and MqsRA toxin-antitoxin system.1 Publication

Gene expression databases

GenevestigatoriP0A968.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

DIPiDIP-47833N.
IntActiP0A968. 39 interactions.
MINTiMINT-1219798.
STRINGi511145.b0880.

Structurei

3D structure databases

ProteinModelPortaliP0A968.
SMRiP0A968. Positions 1-64.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini4 – 6461CSDAdd
BLAST

Sequence similaritiesi

Contains 1 CSD (cold-shock) domain.Curated

Phylogenomic databases

eggNOGiCOG1278.
HOGENOMiHOG000070674.
InParanoidiP0A968.
KOiK03704.
OMAiQQVQFDV.
OrthoDBiEOG618R0J.
PhylomeDBiP0A968.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
InterProiIPR019844. Cold-shock_CS.
IPR012156. Cold_shock_CspA.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012751. CspD.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamiPF00313. CSD. 1 hit.
[Graphical view]
PIRSFiPIRSF002599. Cold_shock_A. 1 hit.
PRINTSiPR00050. COLDSHOCK.
SMARTiSM00357. CSP. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR02381. cspD. 1 hit.
PROSITEiPS00352. COLD_SHOCK. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0A968-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEKGTVKWFN NAKGFGFICP EGGGEDIFAH YSTIQMDGYR TLKAGQSVQF
60 70
DVHQGPKGNH ASVIVPVEVE AAVA
Length:74
Mass (Da):7,969
Last modified:July 19, 2005 - v1
Checksum:iC74AB028135BC22C
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti19 – 191C → E AA sequence (PubMed:9868784).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M31045 Genomic DNA. No translation available.
U00096 Genomic DNA. Translation: AAC73967.1.
AP009048 Genomic DNA. Translation: BAA35599.1.
PIRiH64826.
RefSeqiNP_415401.1. NC_000913.3.
YP_489153.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73967; AAC73967; b0880.
BAA35599; BAA35599; BAA35599.
GeneIDi12934143.
945669.
KEGGiecj:Y75_p0853.
eco:b0880.
PATRICi32116969. VBIEscCol129921_0910.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M31045 Genomic DNA. No translation available.
U00096 Genomic DNA. Translation: AAC73967.1.
AP009048 Genomic DNA. Translation: BAA35599.1.
PIRiH64826.
RefSeqiNP_415401.1. NC_000913.3.
YP_489153.1. NC_007779.1.

3D structure databases

ProteinModelPortaliP0A968.
SMRiP0A968. Positions 1-64.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-47833N.
IntActiP0A968. 39 interactions.
MINTiMINT-1219798.
STRINGi511145.b0880.

Proteomic databases

PaxDbiP0A968.
PRIDEiP0A968.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73967; AAC73967; b0880.
BAA35599; BAA35599; BAA35599.
GeneIDi12934143.
945669.
KEGGiecj:Y75_p0853.
eco:b0880.
PATRICi32116969. VBIEscCol129921_0910.

Organism-specific databases

EchoBASEiEB1102.
EcoGeneiEG11111. cspD.

Phylogenomic databases

eggNOGiCOG1278.
HOGENOMiHOG000070674.
InParanoidiP0A968.
KOiK03704.
OMAiQQVQFDV.
OrthoDBiEOG618R0J.
PhylomeDBiP0A968.

Enzyme and pathway databases

BioCyciEcoCyc:EG11111-MONOMER.
ECOL316407:JW0864-MONOMER.

Miscellaneous databases

PROiP0A968.

Gene expression databases

GenevestigatoriP0A968.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
InterProiIPR019844. Cold-shock_CS.
IPR012156. Cold_shock_CspA.
IPR011129. Cold_shock_prot.
IPR002059. CSP_DNA-bd.
IPR012751. CspD.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamiPF00313. CSD. 1 hit.
[Graphical view]
PIRSFiPIRSF002599. Cold_shock_A. 1 hit.
PRINTSiPR00050. COLDSHOCK.
SMARTiSM00357. CSP. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
TIGRFAMsiTIGR02381. cspD. 1 hit.
PROSITEiPS00352. COLD_SHOCK. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The ATP-dependent Clp protease of Escherichia coli. Sequence of clpA and identification of a Clp-specific substrate."
    Gottesman S., Clark W.P., Maurizi M.R.
    J. Biol. Chem. 265:7886-7893(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Small genes/gene-products in Escherichia coli K-12."
    Wasinger V.C., Humphery-Smith I.
    FEMS Microbiol. Lett. 169:375-382(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-20.
    Strain: K12.
  6. "The product of unr, the highly conserved gene upstream of N-ras, contains multiple repeats similar to the cold-shock domain (CSD), a putative DNA-binding motif."
    Doniger J., Landsman D., Gonda M.A., Wistow G.
    New Biol. 4:389-395(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: SIMILARITY TO OTHER CSD PROTEINS.
  7. "CspD, a novel DNA replication inhibitor induced during the stationary phase in Escherichia coli."
    Yamanaka K., Zheng W., Crooke E., Wang Y.-H., Inouye M.
    Mol. Microbiol. 39:1572-1584(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  8. "Toxins Hha and CspD and small RNA regulator Hfq are involved in persister cell formation through MqsR in Escherichia coli."
    Kim Y., Wood T.K.
    Biochem. Biophys. Res. Commun. 391:209-213(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN PERSISTER CELL FORMATION, DISRUPTION PHENOTYPE.
    Strain: K12 / BW25113.
  9. "Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD."
    Kim Y., Wang X., Zhang X.S., Grigoriu S., Page R., Peti W., Wood T.K.
    Environ. Microbiol. 12:1105-1121(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION AS A TOXIN, INDUCTION.
    Strain: K12 / BW25113.

Entry informationi

Entry nameiCSPD_ECOLI
AccessioniPrimary (citable) accession number: P0A968
Secondary accession number(s): P24245
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2005
Last sequence update: July 19, 2005
Last modified: January 7, 2015
This is version 80 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Binds single-stranded DNA and RNA, but not double-stranded DNA, through hydrophobic interactions without sequence specificity, resulting in a packed structure.

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.