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 20-JAN-2009, entry version 42. 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; Enterobacteriales; 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 MEDLINE=94040726; PubMed=1340475; 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 MEDLINE=94292411; PubMed=8021175; 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 MEDLINE=97061202; PubMed=8905232; DOI=10.1093/dnares/3.3.137; RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., RA Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., RA Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., RA Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., RA Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., RA Yano M., Horiuchi T.; RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome RT corresponding to 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 MEDLINE=97426617; 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., RA Mau B., Shao Y.; RT "The complete genome sequence of Escherichia coli K-12."; RL Science 277:1453-1474(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 RT MG1655 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 MEDLINE=87115160; PubMed=3027504; DOI=10.1007/BF00430437; RA Nohno T., Saito T., Hong J.; RT "Cloning and complete nucleotide sequence of the Escherichia coli RT glutamine 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, RP AND INDUCTION. RC STRAIN=K12; RX MEDLINE=95075312; PubMed=7984106; 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 RT sigma S 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 MEDLINE=93359166; PubMed=8354462; DOI=10.1016/0378-1097(93)90118-L; 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 MEDLINE=97443975; 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 RT in the genome of Escherichia coli K-12."; RL Electrophoresis 18:1259-1313(1997). RN [11] RP PROTEIN SEQUENCE OF 2-11. RX MEDLINE=98362023; 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 RT mirabilis, PMTR, revealed a possible role of YJAI protein in balancing RT zinc in 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 MEDLINE=22140317; 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 RP SOLUTION. RC STRAIN=ZK1100; RX MEDLINE=22241953; 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 RT ferritin-like 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 / 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 RT 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 RT coupled 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 MEDLINE=98206296; 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 RT protects 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- CC crystal within which chromosomal DNA is condensed and protected CC from diverse damages. It protects DNA from oxidative damage by CC sequestering intracellular Fe(2+) ion and storing it in the form CC of Fe(3+) oxyhydroxide mineral, which can be released after CC reduction. One hydrogen peroxide oxidizes two Fe(2+) ions, which CC prevents hydroxyl radical production by the Fenton reaction. Dps CC also protects the cell from UV and gamma irradiation, iron and CC copper toxicity, thermal stress and acid and base shocks. Also CC shows a weak catalase activity. CC -!- CATALYTIC ACTIVITY: 2 Fe(2+) + H(2)O(2) + 2 H(+) = 2 Fe(3+) + 2 CC H(2)O. CC -!- SUBUNIT: Homododecamer. The 12 subunits form a hollow sphere into CC which the mineral iron core of up to 500 Fe(3+) can be deposited. CC -!- INTERACTION: CC P0A862:tpx; NbExp=1; IntAct=EBI-549640, EBI-369411; 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 CC maintaining ongoing dps synthesis during stationary phase. CC -!- DOMAIN: 12 dinuclear ferroxidase centers are located at the CC interfaces between subunits related by 2-fold symmetry axes. The CC lysine-rich N-terminus is required for self-aggregation as well as CC for dps-driven DNA condensation. CC -!- SIMILARITY: Belongs to the dps family. CC ----------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution-NoDerivs License CC ----------------------------------------------------------------------- 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; AP_001443.1; -. DR RefSeq; NP_415333.1; -. 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 PDBsum; 1DPS; -. DR PDBsum; 1F30; -. DR PDBsum; 1F33; -. DR PDBsum; 1JRE; -. DR PDBsum; 1JTS; -. DR PDBsum; 1L8H; -. DR PDBsum; 1L8I; -. DR IntAct; P0ABT2; 28. DR PhosSite; P0ABT2; -. DR SWISS-2DPAGE; P0ABT2; -. DR GeneID; 945101; -. DR GenomeReviews; AP009048_GR; JW0797. DR GenomeReviews; U00096_GR; b0812. DR KEGG; ecj:JW0797; -. DR KEGG; eco:b0812; -. DR EchoBASE; EB1387; -. DR EcoGene; EG11415; dps. DR HOGENOM; P0ABT2; -. DR BioCyc; EcoCyc:EG11415-MON; -. DR GO; GO:0005739; C:mitochondrion; IDA:UniProtKB. DR GO; GO:0003677; F:DNA binding; IEA:HAMAP. DR GO; GO:0008199; F:ferric iron binding; IEA:HAMAP. DR GO; GO:0016491; F:oxidoreductase activity; IEA:HAMAP. DR GO; GO:0005515; F:protein binding; IPI:IntAct. DR GO; GO:0006879; P:cellular iron ion homeostasis; IEA:InterPro. DR GO; GO:0007076; P:mitotic chromosome condensation; IEA:UniProtKB-KW. DR GO; GO:0055114; P:oxidation reduction; IEA:UniProtKB-KW. DR GO; GO:0006950; P:response to stress; IEA:InterPro. DR HAMAP; MF_01441; -; 1. DR InterPro; IPR002177; DPS_DNA_bd. DR InterPro; IPR008331; Ferritin_Dps. DR InterPro; IPR012347; Ferritin_rel. DR Gene3D; G3DSA:1.20.1260.10; Ferritin_rel; 1. DR Pfam; PF00210; Ferritin; 1. DR PIRSF; PIRSF005900; Dps; 1. DR PRINTS; PR01346; HELNAPAPROT. DR ProDom; PD149803; DPS; 1. DR PROSITE; PS00818; DPS_1; 1. DR PROSITE; PS00819; DPS_2; 1. PE 1: Evidence at protein level; KW 3D-structure; Complete proteome; Cytoplasm; Direct protein sequencing; KW DNA condensation; DNA-binding; Iron; Iron storage; Metal-binding; KW Oxidoreductase. FT INIT_MET 1 1 Removed. FT CHAIN 2 167 DNA protection during starvation protein. FT /FTId=PRO_0000201650. FT METAL 51 51 Iron 1; shared with dodecameric partner. FT METAL 78 78 Iron 1. FT METAL 82 82 Iron 1. FT METAL 82 82 Iron 2 (Probable). FT CONFLICT 18 18 R -> N (in Ref. 8; AA sequence). FT CONFLICT 68 68 G -> A (in Ref. 2; AAA21855). FT TURN 10 12 FT HELIX 23 52 FT HELIX 59 86 FT HELIX 95 101 FT HELIX 114 138 FT HELIX 142 164 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 //