DPS_ECOLI
ID DPS_ECOLI Reviewed; 167 AA.
AC P0ABT2; P27430;
DT 25-OCT-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 141.
DE RecName: Full=DNA protection during starvation protein;
DE EC=1.16.-.-;
GN Name=dps; Synonyms=pexB, vtm; OrderedLocusNames=b0812, JW0797;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], DNA-BINDING, AND FUNCTION IN
RP STATIONARY-PHASE SPECIFIC DNA PROTECTION FROM OXIDATIVE STRESS.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=1340475; DOI=10.1101/gad.6.12b.2646;
RA Almiron M., Link A.J., Furlong D., Kolter R.;
RT "A novel DNA-binding protein with regulatory and protective roles in
RT starved Escherichia coli.";
RL Genes Dev. 6:2646-2654(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8021175; DOI=10.1128/jb.176.13.3928-3935.1994;
RA Lomovskaya O.L., Kidwell J.P., Matin A.;
RT "Characterization of the sigma 38-dependent expression of a core
RT Escherichia coli starvation gene, pexB.";
RL J. Bacteriol. 176:3928-3935(1994).
RN [3]
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 [4]
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 [5]
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 [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 80-167.
RC STRAIN=K12;
RA Nohno T.;
RL Submitted (JAN-1989) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 143-167.
RC STRAIN=K12;
RX PubMed=3027504; DOI=10.1007/bf00430437;
RA Nohno T., Saito T., Hong J.;
RT "Cloning and complete nucleotide sequence of the Escherichia coli glutamine
RT permease operon (glnHPQ).";
RL Mol. Gen. Genet. 205:260-269(1986).
RN [8]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-17, PROTEIN SEQUENCE OF 2-20, AND
RP INDUCTION.
RC STRAIN=K12;
RX PubMed=7984106; DOI=10.1111/j.1365-2958.1994.tb00421.x;
RA Altuvia S., Almiron M., Huisman G.W., Kolter R., Storz G.;
RT "The dps promoter is activated by OxyR during growth and by IHF and sigma S
RT in stationary phase.";
RL Mol. Microbiol. 13:265-272(1994).
RN [9]
RP PROTEIN SEQUENCE OF 2-13.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8354462; DOI=10.1111/j.1574-6968.1993.tb06338.x;
RA Foster S.J.;
RT "Purification and characterization of an 'actomyosin' complex from
RT Escherichia coli W3110.";
RL FEMS Microbiol. Lett. 110:295-298(1993).
RN [10]
RP PROTEIN SEQUENCE OF 2-13.
RC STRAIN=K12 / EMG2;
RX PubMed=9298646; DOI=10.1002/elps.1150180807;
RA Link A.J., Robison K., Church G.M.;
RT "Comparing the predicted and observed properties of proteins encoded in the
RT genome of Escherichia coli K-12.";
RL Electrophoresis 18:1259-1313(1997).
RN [11]
RP PROTEIN SEQUENCE OF 2-11.
RX PubMed=9694902; DOI=10.1074/jbc.273.33.21393;
RA Noll M., Petrukhin K., Lutsenko S.;
RT "Identification of a novel transcription regulator from Proteus mirabilis,
RT PMTR, revealed a possible role of YJAI protein in balancing zinc in
RT Escherichia coli.";
RL J. Biol. Chem. 273:21393-21401(1998).
RN [12]
RP IDENTIFICATION OF GENE.
RA Kolter R.;
RT "Life and death in stationary phase.";
RL ASM News 58:75-79(1992).
RN [13]
RP FUNCTION IN DNA PROTECTION BY DNA-DPS CO-CRYSTALLIZATION.
RC STRAIN=SF101;
RX PubMed=10403254; DOI=10.1038/21918;
RA Wolf S.G., Frenkiel D., Arad T., Finkel S.E., Kolter R., Minsky A.;
RT "DNA protection by stress-induced biocrystallization.";
RL Nature 400:83-85(1999).
RN [14]
RP CHARACTERIZATION AS AN IRON STORAGE PROTEIN.
RX PubMed=12016214; DOI=10.1074/jbc.m202094200;
RA Zhao G., Ceci P., Ilari A., Giangiacomo L., Laue T.M., Chiancone E.,
RA Chasteen N.D.;
RT "Iron and hydrogen peroxide detoxification properties of DNA-binding
RT protein from starved cells. A ferritin-like DNA-binding protein of
RT Escherichia coli.";
RL J. Biol. Chem. 277:27689-27696(2002).
RN [15]
RP CRYSTALLIZATION, AND KINETICS OF IRON RELEASE IN CRYSTALS AND IN SOLUTION.
RC STRAIN=ZK1100;
RX PubMed=12163499; DOI=10.1074/jbc.m206186200;
RA Ilari A., Ceci P., Ferrari D., Rossi G.L., Chiancone E.;
RT "Iron incorporation into Escherichia coli Dps gives rise to a ferritin-like
RT microcrystalline core.";
RL J. Biol. Chem. 277:37619-37623(2002).
RN [16]
RP REGULATION OF DPS LEVELS BY CLPXP AND CLPAP.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=12950924; DOI=10.1046/j.1365-2958.2003.03644.x;
RA Stephani K., Weichart D., Hengge R.;
RT "Dynamic control of Dps protein levels by ClpXP and ClpAP proteases in
RT Escherichia coli.";
RL Mol. Microbiol. 49:1605-1614(2003).
RN [17]
RP FUNCTION IN THE PROTECTION OF CELLS AGAINST MULTIPLE STRESSES.
RC STRAIN=K12 / W3110 / ZK126;
RX PubMed=15205421; DOI=10.1128/jb.186.13.4192-4198.2004;
RA Nair S., Finkel S.E.;
RT "Dps protects cells against multiple stresses during stationary phase.";
RL J. Bacteriol. 186:4192-4198(2004).
RN [18]
RP FUNCTION IN DNA CONDENSATION.
RC STRAIN=BL21-DE3;
RX PubMed=15534364; DOI=10.1093/nar/gkh915;
RA Ceci P., Cellai S., Falvo E., Rivetti C., Rossi G.L., Chiancone E.;
RT "DNA condensation and self-aggregation of Escherichia coli Dps are coupled
RT phenomena related to the properties of the N-terminus.";
RL Nucleic Acids Res. 32:5935-5944(2004).
RN [19]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF MUTANT CYS-164, AND SUBUNIT.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9546221; DOI=10.1038/nsb0498-294;
RA Grant R.A., Filman D.J., Finkel S.E., Kolter R., Hogle J.M.;
RT "The crystal structure of Dps, a ferritin homolog that binds and protects
RT DNA.";
RL Nat. Struct. Biol. 5:294-303(1998).
RN [20]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) IN COMPLEX WITH METAL IONS, AND
RP SUBUNIT.
RA Luo J., Liu D., White M.A., Fox R.O.;
RT "The structural basis for DNA protection by E. coli DPS protein.";
RL Submitted (JUN-2003) to the PDB data bank.
CC -!- FUNCTION: During stationary phase, binds the chromosome non-
CC specifically, forming a highly ordered and stable dps-DNA co-crystal
CC within which chromosomal DNA is condensed and protected from diverse
CC damages. It protects DNA from oxidative damage by sequestering
CC intracellular Fe(2+) ion and storing it in the form of Fe(3+)
CC oxyhydroxide mineral, which can be released after reduction. One
CC hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl
CC radical production by the Fenton reaction. Dps also protects the cell
CC from UV and gamma irradiation, iron and copper toxicity, thermal stress
CC and acid and base shocks. Also shows a weak catalase activity.
CC {ECO:0000269|PubMed:10403254, ECO:0000269|PubMed:1340475,
CC ECO:0000269|PubMed:15205421, ECO:0000269|PubMed:15534364}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 Fe(2+) + 2 H(+) + H2O2 = 2 Fe(3+) + 2 H2O;
CC Xref=Rhea:RHEA:48712, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16240, ChEBI:CHEBI:29033, ChEBI:CHEBI:29034;
CC -!- SUBUNIT: Homododecamer. The 12 subunits form a hollow sphere into which
CC the mineral iron core of up to 500 Fe(3+) can be deposited.
CC {ECO:0000269|PubMed:9546221, ECO:0000269|Ref.20}.
CC -!- INTERACTION:
CC P0ABT2; P0A8Q6: clpS; NbExp=5; IntAct=EBI-549640, EBI-561456;
CC P0ABT2; P03004: dnaA; NbExp=2; IntAct=EBI-549640, EBI-548951;
CC P0ABT2; P0ABT2: dps; NbExp=3; IntAct=EBI-549640, EBI-549640;
CC -!- SUBCELLULAR LOCATION: Cytoplasm, nucleoid.
CC -!- INDUCTION: Induced by RpoS and IHF in the early stationary phase.
CC Induced by OxyR in response to oxidative stress during exponential
CC phase. ClpXP probably directly regulate proteolysis of dps during
CC exponential phase. ClpAP seems to play an indirect role in maintaining
CC ongoing dps synthesis during stationary phase.
CC {ECO:0000269|PubMed:7984106}.
CC -!- DOMAIN: 12 dinuclear ferroxidase centers are located at the interfaces
CC between subunits related by 2-fold symmetry axes. The lysine-rich N-
CC terminus is required for self-aggregation as well as for dps-driven DNA
CC condensation.
CC -!- SIMILARITY: Belongs to the Dps family. {ECO:0000305}.
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DR EMBL; X69337; CAA49169.1; -; Genomic_DNA.
DR EMBL; U04242; AAA21855.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73899.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35484.1; -; Genomic_DNA.
DR EMBL; X14180; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; A46401; A46401.
DR RefSeq; NP_415333.1; NC_000913.3.
DR RefSeq; WP_000100800.1; NZ_STEB01000019.1.
DR PDB; 1DPS; X-ray; 1.60 A; A/B/C/D/E/F/G/H/I/J/K/L=1-167.
DR PDB; 1F30; X-ray; 2.85 A; A/B/C/D/E/F/G/H/I/J/K/L=1-167.
DR PDB; 1F33; X-ray; 2.60 A; A/B/C/D/E/F/G/H/I/J/K/L=1-167.
DR PDB; 1JRE; X-ray; 2.65 A; A/B/C/D/E/F/G/H/I/J/K/L=1-167.
DR PDB; 1JTS; X-ray; 2.60 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X=1-167.
DR PDB; 1L8H; X-ray; 3.20 A; A/B/C/D/E/F/G/H/I/J/K/L=1-167.
DR PDB; 1L8I; X-ray; 3.00 A; A/B/C/D/E/F/G/H/I/J/K/L=1-167.
DR PDB; 2W9R; X-ray; 1.70 A; B=6-16.
DR PDB; 3O2H; X-ray; 1.70 A; B=6-16.
DR PDB; 5XGO; X-ray; 1.99 A; A/B/C/D/E/F/G/H/I/J/K/L=1-163.
DR PDB; 6QVX; X-ray; 2.20 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X=9-167.
DR PDB; 6ZGL; EM; 1.92 A; A/B/C/D/E/F/G/H/I/J/K/L=1-167.
DR PDB; 7AQS; X-ray; 2.80 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X=1-167.
DR PDBsum; 1DPS; -.
DR PDBsum; 1F30; -.
DR PDBsum; 1F33; -.
DR PDBsum; 1JRE; -.
DR PDBsum; 1JTS; -.
DR PDBsum; 1L8H; -.
DR PDBsum; 1L8I; -.
DR PDBsum; 2W9R; -.
DR PDBsum; 3O2H; -.
DR PDBsum; 5XGO; -.
DR PDBsum; 6QVX; -.
DR PDBsum; 6ZGL; -.
DR PDBsum; 7AQS; -.
DR AlphaFoldDB; P0ABT2; -.
DR SASBDB; P0ABT2; -.
DR SMR; P0ABT2; -.
DR BioGRID; 4259973; 23.
DR ComplexPortal; CPX-1948; dnaA-dps DNA replication initiation inhibitory complex.
DR DIP; DIP-35919N; -.
DR IntAct; P0ABT2; 37.
DR MINT; P0ABT2; -.
DR STRING; 511145.b0812; -.
DR SWISS-2DPAGE; P0ABT2; -.
DR jPOST; P0ABT2; -.
DR PaxDb; P0ABT2; -.
DR PRIDE; P0ABT2; -.
DR EnsemblBacteria; AAC73899; AAC73899; b0812.
DR EnsemblBacteria; BAA35484; BAA35484; BAA35484.
DR GeneID; 67413850; -.
DR GeneID; 945101; -.
DR KEGG; ecj:JW0797; -.
DR KEGG; eco:b0812; -.
DR PATRIC; fig|1411691.4.peg.1466; -.
DR EchoBASE; EB1387; -.
DR eggNOG; COG0783; Bacteria.
DR HOGENOM; CLU_098183_1_2_6; -.
DR InParanoid; P0ABT2; -.
DR OMA; DDYSIGR; -.
DR PhylomeDB; P0ABT2; -.
DR BioCyc; EcoCyc:EG11415-MON; -.
DR EvolutionaryTrace; P0ABT2; -.
DR PRO; PR:P0ABT2; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-UniRule.
DR GO; GO:1990084; C:DnaA-Dps complex; IPI:ComplexPortal.
DR GO; GO:0016020; C:membrane; HDA:UniProtKB.
DR GO; GO:0009295; C:nucleoid; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IDA:EcoliWiki.
DR GO; GO:0008199; F:ferric iron binding; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0016722; F:oxidoreductase activity, acting on metal ions; IEA:InterPro.
DR GO; GO:0006879; P:cellular iron ion homeostasis; IEA:UniProtKB-KW.
DR GO; GO:0030261; P:chromosome condensation; IEA:UniProtKB-KW.
DR GO; GO:0032297; P:negative regulation of DNA-templated DNA replication initiation; IDA:ComplexPortal.
DR GO; GO:0042594; P:response to starvation; IMP:EcoCyc.
DR CDD; cd01043; DPS; 1.
DR Gene3D; 1.20.1260.10; -; 1.
DR HAMAP; MF_01441; Dps; 1.
DR InterPro; IPR002177; DPS_DNA-bd.
DR InterPro; IPR023188; DPS_DNA-bd_CS.
DR InterPro; IPR023067; Dps_gammaproteobac.
DR InterPro; IPR012347; Ferritin-like.
DR InterPro; IPR009078; Ferritin-like_SF.
DR InterPro; IPR008331; Ferritin_DPS_dom.
DR PANTHER; PTHR42932; PTHR42932; 1.
DR Pfam; PF00210; Ferritin; 1.
DR PIRSF; PIRSF005900; Dps; 1.
DR PRINTS; PR01346; HELNAPAPROT.
DR SUPFAM; SSF47240; SSF47240; 1.
DR PROSITE; PS00818; DPS_1; 1.
DR PROSITE; PS00819; DPS_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; DNA condensation;
KW DNA-binding; Iron; Iron storage; Metal-binding; Oxidoreductase;
KW Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:7984106,
FT ECO:0000269|PubMed:8354462, ECO:0000269|PubMed:9298646,
FT ECO:0000269|PubMed:9694902"
FT CHAIN 2..167
FT /note="DNA protection during starvation protein"
FT /id="PRO_0000201650"
FT BINDING 51
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /ligand_note="ligand shared between two dodecameric
FT partners"
FT BINDING 78
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /ligand_note="ligand shared between two dodecameric
FT partners"
FT /note="in other chain"
FT BINDING 82
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /ligand_note="ligand shared between two dodecameric
FT partners"
FT /note="in other chain"
FT BINDING 82
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000305"
FT CONFLICT 18
FT /note="R -> N (in Ref. 8; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 68
FT /note="G -> A (in Ref. 2; AAA21855)"
FT /evidence="ECO:0000305"
FT TURN 10..12
FT /evidence="ECO:0007829|PDB:1DPS"
FT HELIX 23..52
FT /evidence="ECO:0007829|PDB:1DPS"
FT HELIX 59..86
FT /evidence="ECO:0007829|PDB:1DPS"
FT HELIX 95..101
FT /evidence="ECO:0007829|PDB:1DPS"
FT HELIX 114..138
FT /evidence="ECO:0007829|PDB:1DPS"
FT HELIX 142..164
FT /evidence="ECO:0007829|PDB:1DPS"
SQ SEQUENCE 167 AA; 18695 MW; 596A79B1C6A5E60B CRC64;
MSTAKLVKSK ATNLLYTRND VSDSEKKATV ELLNRQVIQF IDLSLITKQA HWNMRGANFI
AVHEMLDGFR TALIDHLDTM AERAVQLGGV ALGTTQVINS KTPLKSYPLD IHNVQDHLKE
LADRYAIVAN DVRKAIGEAK DDDTADILTA ASRDLDKFLW FIESNIE
