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P80725

- DPS_LISIN

UniProt

P80725 - DPS_LISIN

Protein

DNA protection during starvation protein

Gene

dps

Organism
Listeria innocua serovar 6a (strain CLIP 11262)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 107 (01 Oct 2014)
      Sequence version 1 (01 Nov 1997)
      Previous versions | rss
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    Functioni

    Protects DNA from oxidative damage by sequestering intracellular Fe2+ ion and storing it in the form of Fe3+ oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe2+ ions, which prevents hydroxyl radical production by the Fenton reaction. Does not bind DNA.3 Publications

    Catalytic activityi

    2 Fe2+ + H2O2 + 2 H+ = 2 Fe3+ + 2 H2O.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi31 – 311Iron 1; shared with dodecameric partner1 Publication
    Metal bindingi58 – 581Iron 11 Publication
    Metal bindingi62 – 621Iron 11 Publication
    Metal bindingi62 – 621Iron 21 Publication

    GO - Molecular functioni

    1. ferric iron binding Source: InterPro
    2. oxidoreductase activity, oxidizing metal ions Source: InterPro

    GO - Biological processi

    1. cellular iron ion homeostasis Source: UniProtKB-KW
    2. response to stress Source: InterPro

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Iron storage

    Keywords - Ligandi

    Iron, Metal-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA protection during starvation protein (EC:1.16.-.-)
    Alternative name(s):
    Ferritin-like protein
    Non-heme iron-containing ferritin
    Gene namesi
    Name:dps
    Synonyms:flp, fri
    Ordered Locus Names:lin0942
    OrganismiListeria innocua serovar 6a (strain CLIP 11262)
    Taxonomic identifieri272626 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesListeriaceaeListeria
    ProteomesiUP000002513: Chromosome

    Organism-specific databases

    GenoListiLIN0942.

    Subcellular locationi

    Cytoplasm By similarity

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi31 – 311H → G: Slight decrease in DNA protection and significant decrease in iron affinity. Retains only one third of wild-type DNA protection and loses iron binding ability; when associated with G-43. 1 Publication
    Mutagenesisi43 – 431H → G: Slight decrease in DNA protection and significant decrease iron affinity. Retains only one third of wild-type DNA protection and loses iron-binding ability; when associated with G-31. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 156156DNA protection during starvation proteinPRO_0000201657Add
    BLAST

    Expressioni

    Inductioni

    By iron limitation and stationary growth phase.1 Publication

    Interactioni

    Subunit structurei

    Homododecamer. The 12 subunits form a hollow sphere into which the mineral iron core of up to 500 Fe3+ can be deposited.1 Publication

    Protein-protein interaction databases

    STRINGi272626.lin0942.

    Structurei

    Secondary structure

    1
    156
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi9 – 3325
    Helixi39 – 6628
    Helixi75 – 817
    Helixi95 – 12329
    Helixi126 – 14924

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1QGHX-ray2.35A/B/C/D/E/F/G/H/I/J/K/L1-156[»]
    2BJYX-ray2.60A/B/C/D/E/F/G/H/I/J/K/L1-156[»]
    2BK6X-ray2.19A/B/C/D/E/F1-156[»]
    2BKCX-ray2.30A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/X/Y1-156[»]
    ProteinModelPortaliP80725.
    SMRiP80725. Positions 7-156.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP80725.

    Family & Domainsi

    Domaini

    12 di-nuclear ferroxidase centers are located at the interfaces between subunits related by 2-fold symmetry axes.

    Sequence similaritiesi

    Belongs to the Dps family.Curated

    Phylogenomic databases

    eggNOGiCOG0783.
    HOGENOMiHOG000273542.
    KOiK04047.
    OMAiVEGICEM.
    OrthoDBiEOG6Z9B6G.

    Family and domain databases

    Gene3Di1.20.1260.10. 1 hit.
    InterProiIPR002177. DPS_DNA-bd.
    IPR023188. DPS_DNA-bd_CS.
    IPR009078. Ferritin-like_SF.
    IPR012347. Ferritin-rel.
    IPR008331. Ferritin_DPS_dom.
    [Graphical view]
    PfamiPF00210. Ferritin. 1 hit.
    [Graphical view]
    PIRSFiPIRSF005900. Dps. 1 hit.
    PRINTSiPR01346. HELNAPAPROT.
    SUPFAMiSSF47240. SSF47240. 1 hit.
    PROSITEiPS00818. DPS_1. 1 hit.
    PS00819. DPS_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P80725-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKTINSVDTK EFLNHQVANL NVFTVKIHQI HWYMRGHNFF TLHEKMDDLY    50
    SEFGEQMDEV AERLLAIGGS PFSTLKEFLE NASVEEAPYT KPKTMDQLME 100
    DLVGTLELLR DEYKQGIELT DKEGDDVTND MLIAFKASID KHIWMFKAFL 150
    GKAPLE 156
    Length:156
    Mass (Da):18,049
    Last modified:November 1, 1997 - v1
    Checksum:i5FC9FFF5EE7FB6F8
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti63 – 631R → L(PubMed:12383509)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ244014 Genomic DNA. Translation: CAB65175.2.
    AL596167 Genomic DNA. Translation: CAC96173.1.
    PIRiAE1550.
    RefSeqiNP_470279.1. NC_003212.1.
    WP_003761404.1. NC_003212.1.

    Genome annotation databases

    EnsemblBacteriaiCAC96173; CAC96173; CAC96173.
    GeneIDi1129452.
    KEGGilin:lin0942.
    PATRICi20298599. VBILisInn102668_0967.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AJ244014 Genomic DNA. Translation: CAB65175.2 .
    AL596167 Genomic DNA. Translation: CAC96173.1 .
    PIRi AE1550.
    RefSeqi NP_470279.1. NC_003212.1.
    WP_003761404.1. NC_003212.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1QGH X-ray 2.35 A/B/C/D/E/F/G/H/I/J/K/L 1-156 [» ]
    2BJY X-ray 2.60 A/B/C/D/E/F/G/H/I/J/K/L 1-156 [» ]
    2BK6 X-ray 2.19 A/B/C/D/E/F 1-156 [» ]
    2BKC X-ray 2.30 A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/X/Y 1-156 [» ]
    ProteinModelPortali P80725.
    SMRi P80725. Positions 7-156.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 272626.lin0942.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CAC96173 ; CAC96173 ; CAC96173 .
    GeneIDi 1129452.
    KEGGi lin:lin0942.
    PATRICi 20298599. VBILisInn102668_0967.

    Organism-specific databases

    GenoListi LIN0942.

    Phylogenomic databases

    eggNOGi COG0783.
    HOGENOMi HOG000273542.
    KOi K04047.
    OMAi VEGICEM.
    OrthoDBi EOG6Z9B6G.

    Miscellaneous databases

    EvolutionaryTracei P80725.

    Family and domain databases

    Gene3Di 1.20.1260.10. 1 hit.
    InterProi IPR002177. DPS_DNA-bd.
    IPR023188. DPS_DNA-bd_CS.
    IPR009078. Ferritin-like_SF.
    IPR012347. Ferritin-rel.
    IPR008331. Ferritin_DPS_dom.
    [Graphical view ]
    Pfami PF00210. Ferritin. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF005900. Dps. 1 hit.
    PRINTSi PR01346. HELNAPAPROT.
    SUPFAMi SSF47240. SSF47240. 1 hit.
    PROSITEi PS00818. DPS_1. 1 hit.
    PS00819. DPS_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "A novel non-heme iron-binding ferritin related to the DNA-binding proteins of the Dps family in Listeria innocua."
      Bozzi M., Mignogna G., Stefanini S., Barra D., Longhi C., Valenti P., Chiancone E.
      J. Biol. Chem. 272:3259-3265(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE, FUNCTION.
    2. "The expression of the dodecameric ferritin in Listeria spp. is induced by iron limitation and stationary growth phase."
      Polidoro M., De Biase D., Montagnini B., Guarrera L., Cavallo S., Valenti P., Stefanini S., Chiancone E.
      Gene 296:121-128(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, INDUCTION.
      Strain: LS1.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: CLIP 11262.
    4. "The so-called Listeria innocua ferritin is a Dps protein. Iron incorporation, detoxification, and DNA protection properties."
      Su M., Cavallo S., Stefanini S., Chiancone E., Chasteen N.D.
      Biochemistry 44:5572-5578(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN DNA PROTECTION, IRON INCORPORATION.
    5. "The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site."
      Ilari A., Stefanini S., Chiancone E., Tsernoglou D.
      Nat. Struct. Biol. 7:38-43(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEX WITH IRON, SUBUNIT.
    6. "The unusual intersubunit ferroxidase center of Listeria innocua Dps is required for hydrogen peroxide detoxification but not for iron uptake. A study with site-specific mutants."
      Ilari A., Latella M.C., Ceci P., Ribacchi F., Su M., Giangiacomo L., Stefanini S., Chasteen N.D., Chiancone E.
      Biochemistry 44:5579-5587(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.19 ANGSTROMS) OF MUTANTS GLY-31 AND GLY-43, MUTAGENESIS OF HIS-31 AND HIS-43.

    Entry informationi

    Entry nameiDPS_LISIN
    AccessioniPrimary (citable) accession number: P80725
    Secondary accession number(s): Q9RE06
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1997
    Last modified: October 1, 2014
    This is version 107 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3