DPS1_DEIRA
ID DPS1_DEIRA Reviewed; 207 AA.
AC Q9RS64;
DT 17-OCT-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=DNA protection during starvation protein 1;
DE EC=1.16.-.-;
GN Name=dps1; Synonyms=dps-1; OrderedLocusNames=DR_2263;
OS Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG
OS 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422).
OC Bacteria; Deinococcus-Thermus; Deinococci; Deinococcales; Deinococcaceae;
OC Deinococcus.
OX NCBI_TaxID=243230;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=10567266; DOI=10.1126/science.286.5444.1571;
RA White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D.,
RA Dodson R.J., Haft D.H., Gwinn M.L., Nelson W.C., Richardson D.L.,
RA Moffat K.S., Qin H., Jiang L., Pamphile W., Crosby M., Shen M.,
RA Vamathevan J.J., Lam P., McDonald L.A., Utterback T.R., Zalewski C.,
RA Makarova K.S., Aravind L., Daly M.J., Minton K.W., Fleischmann R.D.,
RA Ketchum K.A., Nelson K.E., Salzberg S.L., Smith H.O., Venter J.C.,
RA Fraser C.M.;
RT "Genome sequence of the radioresistant bacterium Deinococcus radiodurans
RT R1.";
RL Science 286:1571-1577(1999).
RN [2]
RP DNA-BINDING, FUNCTION IN DNA PROTECTION, AND SUBUNIT.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=15755446; DOI=10.1016/j.jmb.2005.01.055;
RA Grove A., Wilkinson S.P.;
RT "Differential DNA binding and protection by dimeric and dodecameric forms
RT of the ferritin homolog Dps from Deinococcus radiodurans.";
RL J. Mol. Biol. 347:495-508(2005).
CC -!- FUNCTION: Protects DNA from oxidative damage by sequestering
CC intracellular Fe(2+) ion and storing it in the form of Fe(3+)
CC oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions,
CC which prevents hydroxyl radical production by the Fenton reaction (By
CC similarity). Both oligomeric forms of dps exhibit ferroxidase activity
CC and DNA binding. Dodecameric dps is capable of Fe(2+)
CC oxidation/mineralization. Only dimeric dps affords efficient DNA
CC protection against hydroxyl radical-mediated cleavage. {ECO:0000250,
CC ECO:0000269|PubMed:15755446}.
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: The 12 subunits form a hollow sphere into which the mineral
CC iron core of up to 500 Fe(3+) can be deposited (By similarity). The
CC homododecameric forms at higher concentration of salt, the homodimeric
CC form under reducing, low-salt conditions. The assembly of the dodecamer
CC is irreversible. {ECO:0000250, ECO:0000269|PubMed:15755446}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm, nucleoid {ECO:0000250}.
CC -!- DOMAIN: 12 di-nuclear ferroxidase centers are located at the interfaces
CC between subunits related by 2-fold symmetry axes. {ECO:0000250}.
CC -!- MISCELLANEOUS: Dodecameric dps forms large aggregates upon binding to
CC DNA.
CC -!- MISCELLANEOUS: Addition of Ca(2+) to dodecameric dps can result in the
CC reduction of bound Fe(3+).
CC -!- SIMILARITY: Belongs to the Dps family. {ECO:0000305}.
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DR EMBL; AE000513; AAF11811.1; -; Genomic_DNA.
DR PIR; B75294; B75294.
DR RefSeq; NP_295984.1; NC_001263.1.
DR RefSeq; WP_010888891.1; NZ_CP015081.1.
DR PDB; 2C2F; X-ray; 1.61 A; A=1-207.
DR PDB; 2C2U; X-ray; 1.10 A; A=1-207.
DR PDB; 2F7N; X-ray; 2.00 A; A=1-207.
DR PDBsum; 2C2F; -.
DR PDBsum; 2C2U; -.
DR PDBsum; 2F7N; -.
DR AlphaFoldDB; Q9RS64; -.
DR SASBDB; Q9RS64; -.
DR SMR; Q9RS64; -.
DR STRING; 243230.DR_2263; -.
DR EnsemblBacteria; AAF11811; AAF11811; DR_2263.
DR KEGG; dra:DR_2263; -.
DR PATRIC; fig|243230.17.peg.2491; -.
DR eggNOG; COG0783; Bacteria.
DR HOGENOM; CLU_098183_0_1_0; -.
DR InParanoid; Q9RS64; -.
DR OMA; LYLQTHN; -.
DR OrthoDB; 1742631at2; -.
DR EvolutionaryTrace; Q9RS64; -.
DR Proteomes; UP000002524; Chromosome I.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-KW.
DR GO; GO:0009295; C:nucleoid; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0008199; F:ferric iron binding; IEA:InterPro.
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 CDD; cd01043; DPS; 1.
DR Gene3D; 1.20.1260.10; -; 1.
DR InterPro; IPR002177; DPS_DNA-bd.
DR InterPro; IPR023188; DPS_DNA-bd_CS.
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 PRINTS; PR01346; HELNAPAPROT.
DR SUPFAM; SSF47240; SSF47240; 1.
DR PROSITE; PS00818; DPS_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; DNA-binding; Iron; Iron storage; Metal-binding;
KW Oxidoreductase; Reference proteome.
FT CHAIN 1..207
FT /note="DNA protection during starvation protein 1"
FT /id="PRO_0000253326"
FT REGION 1..31
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 83
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 /evidence="ECO:0000250"
FT BINDING 110
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 /evidence="ECO:0000250"
FT BINDING 114
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 /evidence="ECO:0000250"
FT BINDING 114
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT HELIX 33..35
FT /evidence="ECO:0007829|PDB:2C2U"
FT HELIX 55..85
FT /evidence="ECO:0007829|PDB:2C2U"
FT HELIX 91..105
FT /evidence="ECO:0007829|PDB:2C2U"
FT HELIX 108..118
FT /evidence="ECO:0007829|PDB:2C2U"
FT HELIX 127..133
FT /evidence="ECO:0007829|PDB:2C2U"
FT HELIX 146..173
FT /evidence="ECO:0007829|PDB:2C2U"
FT HELIX 177..201
FT /evidence="ECO:0007829|PDB:2C2U"
SQ SEQUENCE 207 AA; 23020 MW; C0CD6D2F9BC566E3 CRC64;
MTKKSTKSEA ASKTKKSGVP ETGAQGVRAG GADHADAAHL GTVNNALVNH HYLEEKEFQT
VAETLQRNLA TTISLYLKFK KYHWDIRGRF FRDLHLAYDE FIAEIFPSID EQAERLVALG
GSPLAAPADL ARYSTVQVPQ ETVRDARTQV ADLVQDLSRV GKGYRDDSQA CDEANDPVTA
DMYNGYAATI DKIRWMLQAI MDDERLD
