ID   CSPD_ECOLI              Reviewed;          74 AA.
AC   P0A968; P24245;
DT   19-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT   19-JUL-2005, sequence version 1.
DT   24-JAN-2024, entry version 130.
DE   RecName: Full=Cold shock-like protein CspD;
DE            Short=CSP-D;
GN   Name=cspD; Synonyms=cspH, ybjA; OrderedLocusNames=b0880, JW0864;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=K12;
RX   PubMed=2186030; DOI=10.1016/s0021-9258(19)39014-3;
RA   Gottesman S., Clark W.P., Maurizi M.R.;
RT   "The ATP-dependent Clp protease of Escherichia coli. Sequence of clpA and
RT   identification of a Clp-specific substrate.";
RL   J. Biol. Chem. 265:7886-7893(1990).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA   Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA   Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA   Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA   Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA   Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA   Horiuchi T.;
RT   "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT   the 12.7-28.0 min region on the linkage map.";
RL   DNA Res. 3:137-155(1996).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA   Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1462(1997).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT   and W3110.";
RL   Mol. Syst. Biol. 2:E1-E5(2006).
RN   [5]
RP   PROTEIN SEQUENCE OF 1-20.
RC   STRAIN=K12;
RX   PubMed=9868784; DOI=10.1111/j.1574-6968.1998.tb13343.x;
RA   Wasinger V.C., Humphery-Smith I.;
RT   "Small genes/gene-products in Escherichia coli K-12.";
RL   FEMS Microbiol. Lett. 169:375-382(1998).
RN   [6]
RP   SIMILARITY TO OTHER CSD PROTEINS.
RX   PubMed=1622933;
RA   Doniger J., Landsman D., Gonda M.A., Wistow G.;
RT   "The product of unr, the highly conserved gene upstream of N-ras, contains
RT   multiple repeats similar to the cold-shock domain (CSD), a putative DNA-
RT   binding motif.";
RL   New Biol. 4:389-395(1992).
RN   [7]
RP   CHARACTERIZATION.
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=11260474; DOI=10.1046/j.1365-2958.2001.02345.x;
RA   Yamanaka K., Zheng W., Crooke E., Wang Y.-H., Inouye M.;
RT   "CspD, a novel DNA replication inhibitor induced during the stationary
RT   phase in Escherichia coli.";
RL   Mol. Microbiol. 39:1572-1584(2001).
RN   [8]
RP   FUNCTION IN PERSISTER CELL FORMATION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=K12 / BW25113;
RX   PubMed=19909729; DOI=10.1016/j.bbrc.2009.11.033;
RA   Kim Y., Wood T.K.;
RT   "Toxins Hha and CspD and small RNA regulator Hfq are involved in persister
RT   cell formation through MqsR in Escherichia coli.";
RL   Biochem. Biophys. Res. Commun. 391:209-213(2010).
RN   [9]
RP   FUNCTION AS A TOXIN, AND INDUCTION.
RC   STRAIN=K12 / BW25113;
RX   PubMed=20105222; DOI=10.1111/j.1462-2920.2009.02147.x;
RA   Kim Y., Wang X., Zhang X.S., Grigoriu S., Page R., Peti W., Wood T.K.;
RT   "Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD.";
RL   Environ. Microbiol. 12:1105-1121(2010).
CC   -!- FUNCTION: Inhibits DNA replication at both initiation and elongation
CC       steps, most probably by binding to the opened, single-stranded regions
CC       at replication forks. Plays a regulatory role in chromosomal
CC       replication in nutrient-depleted cells.
CC   -!- FUNCTION: Involved in persister cell formation, acting downstream of
CC       mRNA interferase (toxin) MqsR. Overproduction is toxic.
CC   -!- SUBUNIT: Homodimer.
CC   -!- INTERACTION:
CC       P0A968; P0AAG0: dppD; NbExp=3; IntAct=EBI-547937, EBI-548206;
CC   -!- SUBCELLULAR LOCATION: Cytoplasm.
CC   -!- INDUCTION: Not induced by cold-shock. Stationary-phase and starvation
CC       inducible, as well as by oxidative stress (30 mM H(2)O(2)). Repressed
CC       by MqsA and MqsRA toxin-antitoxin system.
CC       {ECO:0000269|PubMed:20105222}.
CC   -!- DISRUPTION PHENOTYPE: Deletion represses the production of persister
CC       cells. {ECO:0000269|PubMed:19909729}.
CC   -!- MISCELLANEOUS: Binds single-stranded DNA and RNA, but not double-
CC       stranded DNA, through hydrophobic interactions without sequence
CC       specificity, resulting in a packed structure.
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DR   EMBL; M31045; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; U00096; AAC73967.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAA35599.1; -; Genomic_DNA.
DR   PIR; H64826; H64826.
DR   RefSeq; NP_415401.1; NC_000913.3.
DR   RefSeq; WP_000410785.1; NZ_STEB01000006.1.
DR   AlphaFoldDB; P0A968; -.
DR   SMR; P0A968; -.
DR   BioGRID; 4263137; 734.
DR   BioGRID; 850041; 1.
DR   DIP; DIP-47833N; -.
DR   IntAct; P0A968; 39.
DR   STRING; 511145.b0880; -.
DR   jPOST; P0A968; -.
DR   PaxDb; 511145-b0880; -.
DR   EnsemblBacteria; AAC73967; AAC73967; b0880.
DR   GeneID; 83577193; -.
DR   GeneID; 945669; -.
DR   KEGG; ecj:JW0864; -.
DR   KEGG; eco:b0880; -.
DR   PATRIC; fig|1411691.4.peg.1397; -.
DR   EchoBASE; EB1102; -.
DR   eggNOG; COG1278; Bacteria.
DR   HOGENOM; CLU_117621_0_2_6; -.
DR   InParanoid; P0A968; -.
DR   OMA; HYSTIKM; -.
DR   OrthoDB; 9810590at2; -.
DR   PhylomeDB; P0A968; -.
DR   BioCyc; EcoCyc:EG11111-MONOMER; -.
DR   PRO; PR:P0A968; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR   GO; GO:0003676; F:nucleic acid binding; IBA:GO_Central.
DR   GO; GO:0042803; F:protein homodimerization activity; IDA:EcoCyc.
DR   GO; GO:0003723; F:RNA binding; IDA:EcoCyc.
DR   GO; GO:0003697; F:single-stranded DNA binding; IDA:EcoCyc.
DR   GO; GO:0090729; F:toxin activity; IEA:UniProtKB-KW.
DR   GO; GO:0008156; P:negative regulation of DNA replication; IDA:EcoCyc.
DR   GO; GO:0006355; P:regulation of DNA-templated transcription; IEA:InterPro.
DR   GO; GO:0010468; P:regulation of gene expression; IBA:GO_Central.
DR   GO; GO:0042594; P:response to starvation; IDA:EcoliWiki.
DR   CDD; cd04458; CSP_CDS; 1.
DR   DisProt; DP02900; -.
DR   Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR   InterPro; IPR012156; Cold_shock_CspA.
DR   InterPro; IPR011129; CSD.
DR   InterPro; IPR019844; CSD_1.
DR   InterPro; IPR002059; CSP_DNA-bd.
DR   InterPro; IPR012751; CspD.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   NCBIfam; TIGR02381; cspD; 1.
DR   PANTHER; PTHR11544; COLD SHOCK DOMAIN CONTAINING PROTEINS; 1.
DR   PANTHER; PTHR11544:SF141; COLD SHOCK-LIKE PROTEIN CSPD; 1.
DR   Pfam; PF00313; CSD; 1.
DR   PIRSF; PIRSF002599; Cold_shock_A; 1.
DR   PRINTS; PR00050; COLDSHOCK.
DR   SMART; SM00357; CSP; 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR   PROSITE; PS00352; CSD_1; 1.
DR   PROSITE; PS51857; CSD_2; 1.
PE   1: Evidence at protein level;
KW   Cytoplasm; Direct protein sequencing; DNA replication inhibitor;
KW   DNA-binding; Reference proteome; RNA-binding; Toxin.
FT   CHAIN           1..74
FT                   /note="Cold shock-like protein CspD"
FT                   /id="PRO_0000100248"
FT   DOMAIN          4..64
FT                   /note="CSD"
FT   CONFLICT        19
FT                   /note="C -> E (in Ref. 5; AA sequence)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   74 AA;  7969 MW;  C74AB028135BC22C CRC64;
     MEKGTVKWFN NAKGFGFICP EGGGEDIFAH YSTIQMDGYR TLKAGQSVQF DVHQGPKGNH
     ASVIVPVEVE AAVA
//