Cold shock-like protein CspD - Escherichia coli (strain K12)

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P0A968 (CSPD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 70. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Cold shock-like protein CspD
Short name=CSP-D

Gene names

Name:	cspD
Synonyms:	cspH, ybjA
Ordered Locus Names:	b0880, JW0864

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	74 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.8 Ref.9 Involved in persister cell formation, acting downstream of mRNA interferase (toxin) MqsR. Overproduction is toxic. Ref.8 Ref.9
Subunit structure	Homodimer.
Subcellular location	Cytoplasm.
Induction	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. Ref.9
Disruption phenotype	Deletion represses the production of persister cells. Ref.8
Miscellaneous	Binds single-stranded DNA and RNA, but not double-stranded DNA, through hydrophobic interactions without sequence specificity, resulting in a packed structure.
Sequence similarities	Contains 1 CSD (cold-shock) domain.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	DNA-binding RNA-binding
Molecular function	DNA replication inhibitor Toxin
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	negative regulation of DNA replication Inferred from direct assay Ref.7. Source: EcoCyc regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro response to starvation Inferred from direct assay PubMed 9260955. Source: EcoliWiki
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	RNA binding Inferred from direct assay Ref.7. Source: EcoCyc single-stranded DNA binding Inferred from direct assay Ref.7. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 74

Cold shock-like protein CspD

PRO_0000100248

Regions

Domain

4 – 64

CSD

Experimental info

Sequence conflict

C → E AA sequence Ref.5

Sequences

Sequence

Length

Mass (Da)

Tools

P0A968 [UniParc].

Last modified July 19, 2005. Version 1.
Checksum: C74AB028135BC22C
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FASTA

7,969

        10         20         30         40         50         60 
MEKGTVKWFN NAKGFGFICP EGGGEDIFAH YSTIQMDGYR TLKAGQSVQF DVHQGPKGNH 

        70 
ASVIVPVEVE AAVA

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map." Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K. Horiuchi T. DNA Res. 3:137-155(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[3]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	M31045 Genomic DNA. No translation available. U00096 Genomic DNA. Translation: AAC73967.1. AP009048 Genomic DNA. Translation: BAA35599.1.
PIR	H64826.
RefSeq	NP_415401.1. NC_000913.2. YP_489153.1. NC_007779.1.
3D structure databases
ProteinModelPortal	P0A968.
SMR	P0A968. Positions 1-64.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-47833N.
IntAct	P0A968. 39 interactions.
MINT	MINT-1219798.
STRING	511145.b0880.
Proteomic databases
PaxDb	P0A968.
PRIDE	P0A968.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAC73967; AAC73967; b0880. BAA35599; BAA35599; BAA35599.
GeneID	12934143. 945669.
KEGG	ecj:Y75_p0853. eco:b0880.
PATRIC	32116969. VBIEscCol129921_0910.
Organism-specific databases
EchoBASE	EB1102.
EcoGene	EG11111. cspD.
Phylogenomic databases
eggNOG	COG1278.
HOGENOM	HOG000070674.
KO	K03704.
OMA	QVVRFDV.
ProtClustDB	PRK09937.
Enzyme and pathway databases
BioCyc	EcoCyc:EG11111-MONOMER. ECOL316407:JW0864-MONOMER.
Gene expression databases
Genevestigator	P0A968.
Family and domain databases
Gene3D	2.40.50.140. 1 hit.
InterPro	IPR019844. Cold-shock_CS. IPR012156. Cold_shock_CspA. IPR011129. Cold_shock_prot. IPR002059. CSP_DNA-bd. IPR012751. CspD. IPR012340. NA-bd_OB-fold. [Graphical view]
Pfam	PF00313. CSD. 1 hit. [Graphical view]
PIRSF	PIRSF002599. Cold_shock_A. 1 hit.
PRINTS	PR00050. COLDSHOCK.
SMART	SM00357. CSP. 1 hit. [Graphical view]
SUPFAM	SSF50249. Nucleic_acid_OB. 1 hit.
TIGRFAMs	TIGR02381. cspD. 1 hit.
PROSITE	PS00352. COLD_SHOCK. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

CSPD_ECOLI

Accession

Primary (citable) accession number: P0A968
Secondary accession number(s): P24245

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 19, 2005
Last sequence update:	July 19, 2005
Last modified:	May 1, 2013
This is version 70 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents