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P80725

- DPS_LISIN

UniProt

P80725 - DPS_LISIN

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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

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
Complete GO annotation...

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-KW
Complete GO annotation...

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 – 3325Combined sources
Helixi39 – 6628Combined sources
Helixi75 – 817Combined sources
Helixi95 – 12329Combined sources
Helixi126 – 14924Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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

        10         20         30         40         50
MKTINSVDTK EFLNHQVANL NVFTVKIHQI HWYMRGHNFF TLHEKMDDLY
60 70 80 90 100
SEFGEQMDEV AERLLAIGGS PFSTLKEFLE NASVEEAPYT KPKTMDQLME
110 120 130 140 150
DLVGTLELLR DEYKQGIELT DKEGDDVTND MLIAFKASID KHIWMFKAFL

GKAPLE
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 109 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