DPS_MYCSM
ID DPS_MYCSM Reviewed; 183 AA.
AC P0C558; Q8VP75;
DT 10-JUL-2007, integrated into UniProtKB/Swiss-Prot.
DT 10-JUL-2007, sequence version 1.
DT 03-AUG-2022, entry version 63.
DE RecName: Full=DNA protection during starvation protein;
DE EC=1.16.-.-;
GN Name=dps;
OS Mycolicibacterium smegmatis (Mycobacterium smegmatis).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycolicibacterium.
OX NCBI_TaxID=1772;
RN [1]
RP FUNCTION IN PROTECTION OF DNA, AND SUBUNIT.
RX PubMed=12466274; DOI=10.1074/jbc.m208825200;
RA Gupta S., Chatterji D.;
RT "Bimodal protection of DNA by Mycobacterium smegmatis DNA-binding protein
RT from stationary phase cells.";
RL J. Biol. Chem. 278:5235-5241(2003).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) IN COMPLEX WITH IRON, AND SUBUNIT.
RX PubMed=15178251; DOI=10.1016/j.jmb.2004.04.042;
RA Roy S., Gupta S., Das S., Sekar K., Chatterji D., Vijayan M.;
RT "X-ray analysis of Mycobacterium smegmatis Dps and a comparative study
RT involving other Dps and Dps-like molecules.";
RL J. Mol. Biol. 339:1103-1113(2004).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH IRON, DNA-BINDING,
RP DNA PROTECTION, AND SUBUNIT.
RC STRAIN=MC2;
RX PubMed=16030020; DOI=10.1074/jbc.m502343200;
RA Ceci P., Ilari A., Falvo E., Giangiacomo L., Chiancone E.;
RT "Reassessment of protein stability, DNA binding, and protection of
RT Mycobacterium smegmatis Dps.";
RL J. Biol. Chem. 280:34776-34785(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). It protects DNA from hydroxyl radical-mediated cleavage.
CC Binds DNA with no apparent sequence specificity without self-
CC aggregation nor promotion of DNA condensation. Is unable to protect DNA
CC from DNase-mediated cleavage. {ECO:0000250,
CC ECO:0000269|PubMed:12466274}.
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 identical subunits form a hollow sphere into which the
CC mineral iron core of up to 500 Fe(3+) can be deposited (By similarity).
CC Homododecamer. {ECO:0000250, ECO:0000269|PubMed:12466274,
CC ECO:0000269|PubMed:15178251, ECO:0000269|PubMed:16030020}.
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.
CC -!- SIMILARITY: Belongs to the Dps family. {ECO:0000305}.
CC -!- CAUTION: The sequence shown here has been extracted from PDB entry
CC 1UVH. {ECO:0000305}.
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DR RefSeq; WP_003897878.1; NZ_UGQO01000001.1.
DR PDB; 1UVH; X-ray; 2.80 A; A/B/C/D=1-183.
DR PDB; 1VEI; X-ray; 2.85 A; A=1-183.
DR PDB; 1VEL; X-ray; 2.99 A; A/B/C/D/E/F=1-183.
DR PDB; 1VEQ; X-ray; 3.98 A; A/B/C/D/E/F/G/H/I/J/K/L=1-183.
DR PDB; 2YW6; X-ray; 2.53 A; A/B/C=1-183.
DR PDB; 2YW7; X-ray; 3.30 A; A/B/C/D/E/F/G/H/I/J=1-183.
DR PDBsum; 1UVH; -.
DR PDBsum; 1VEI; -.
DR PDBsum; 1VEL; -.
DR PDBsum; 1VEQ; -.
DR PDBsum; 2YW6; -.
DR PDBsum; 2YW7; -.
DR AlphaFoldDB; P0C558; -.
DR SMR; P0C558; -.
DR GeneID; 66737739; -.
DR OMA; DDYSIGR; -.
DR EvolutionaryTrace; P0C558; -.
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 PIRSF; PIRSF005900; Dps; 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.
FT CHAIN 1..183
FT /note="DNA protection during starvation protein"
FT /id="PRO_0000253333"
FT REGION 162..183
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 39
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:0000269|PubMed:15178251,
FT ECO:0000269|PubMed:16030020"
FT BINDING 66
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:0000269|PubMed:15178251,
FT ECO:0000269|PubMed:16030020"
FT BINDING 70
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:0000269|PubMed:15178251,
FT ECO:0000269|PubMed:16030020"
FT BINDING 70
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000305|PubMed:15178251,
FT ECO:0000305|PubMed:16030020"
FT HELIX 14..41
FT /evidence="ECO:0007829|PDB:2YW6"
FT STRAND 42..44
FT /evidence="ECO:0007829|PDB:2YW6"
FT HELIX 47..74
FT /evidence="ECO:0007829|PDB:2YW6"
FT HELIX 83..89
FT /evidence="ECO:0007829|PDB:2YW6"
FT STRAND 99..101
FT /evidence="ECO:0007829|PDB:2YW6"
FT HELIX 102..127
FT /evidence="ECO:0007829|PDB:2YW6"
FT TURN 128..130
FT /evidence="ECO:0007829|PDB:2YW6"
FT HELIX 132..156
FT /evidence="ECO:0007829|PDB:2YW6"
FT STRAND 159..161
FT /evidence="ECO:0007829|PDB:1VEI"
SQ SEQUENCE 183 AA; 20270 MW; 3ACB34B43B23F877 CRC64;
MTSFTIPGLS DKKASDVADL LQKQLSTYND LHLTLKHVHW NVVGPNFIGV HEMIDPQVEL
VRGYADEVAE RIATLGKSPK GTPGAIIKDR TWDDYSVERD TVQAHLAALD LVYNGVIEDT
RKSIEKLEDL DLVSQDLLIA HAGELEKFQW FVRAHLESAG GQLTHEGQST EKGAADKARR
KSA
