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Protein

DNA protection during starvation protein 1

Gene

dps1

Organism
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Status
Reviewed-Annotation score: 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 (By similarity). Both oligomeric forms of dps exhibit ferroxidase activity and DNA binding. Dodecameric dps is capable of Fe2+ oxidation/mineralization. Only dimeric dps affords efficient DNA protection against hydroxyl radical-mediated cleavage.By similarity1 Publication

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi83 – 831Iron 1; shared with dodecameric partnerBy similarity
Metal bindingi110 – 1101Iron 1By similarity
Metal bindingi114 – 1141Iron 1By similarity
Metal bindingi114 – 1141Iron 2By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Iron storage

Keywords - Ligandi

DNA-binding, Iron, Metal-binding

Enzyme and pathway databases

BioCyciDRAD243230:GH46-2311-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA protection during starvation protein 1 (EC:1.16.-.-)
Gene namesi
Name:dps1
Synonyms:dps-1
Ordered Locus Names:DR_2263
OrganismiDeinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Taxonomic identifieri243230 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciDeinococcalesDeinococcaceaeDeinococcus
Proteomesi
  • UP000002524 Componenti: Chromosome I

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 207207DNA protection during starvation protein 1PRO_0000253326Add
BLAST

Proteomic databases

PRIDEiQ9RS64.

Interactioni

Subunit structurei

The 12 subunits form a hollow sphere into which the mineral iron core of up to 500 Fe3+ can be deposited (By similarity). The homododecameric forms at higher concentration of salt, the homodimeric form under reducing, low-salt conditions. The assembly of the dodecamer is irreversible.By similarity1 Publication

Protein-protein interaction databases

STRINGi243230.DR_2263.

Structurei

Secondary structure

1
207
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi33 – 353Combined sources
Helixi55 – 8531Combined sources
Helixi91 – 10515Combined sources
Helixi108 – 11811Combined sources
Helixi127 – 1337Combined sources
Helixi146 – 17328Combined sources
Helixi177 – 20125Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2C2FX-ray1.61A1-207[»]
2C2UX-ray1.10A1-207[»]
2F7NX-ray2.00A1-207[»]
ProteinModelPortaliQ9RS64.
SMRiQ9RS64. Positions 30-207.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9RS64.

Family & Domainsi

Domaini

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

Sequence similaritiesi

Belongs to the Dps family.Curated

Phylogenomic databases

eggNOGiENOG4105IJD. Bacteria.
COG0783. LUCA.
HOGENOMiHOG000099528.
InParanoidiQ9RS64.
KOiK04047.
OMAiVWFLFES.
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]
PRINTSiPR01346. HELNAPAPROT.
SUPFAMiSSF47240. SSF47240. 1 hit.
PROSITEiPS00818. DPS_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9RS64-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTKKSTKSEA ASKTKKSGVP ETGAQGVRAG GADHADAAHL GTVNNALVNH
60 70 80 90 100
HYLEEKEFQT VAETLQRNLA TTISLYLKFK KYHWDIRGRF FRDLHLAYDE
110 120 130 140 150
FIAEIFPSID EQAERLVALG GSPLAAPADL ARYSTVQVPQ ETVRDARTQV
160 170 180 190 200
ADLVQDLSRV GKGYRDDSQA CDEANDPVTA DMYNGYAATI DKIRWMLQAI

MDDERLD
Length:207
Mass (Da):23,020
Last modified:May 1, 2000 - v1
Checksum:iC0CD6D2F9BC566E3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000513 Genomic DNA. Translation: AAF11811.1.
PIRiB75294.
RefSeqiNP_295984.1. NC_001263.1.
WP_010888891.1. NC_001263.1.

Genome annotation databases

EnsemblBacteriaiAAF11811; AAF11811; DR_2263.
GeneIDi1800263.
KEGGidra:DR_2263.
PATRICi21632226. VBIDeiRad64572_2491.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000513 Genomic DNA. Translation: AAF11811.1.
PIRiB75294.
RefSeqiNP_295984.1. NC_001263.1.
WP_010888891.1. NC_001263.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2C2FX-ray1.61A1-207[»]
2C2UX-ray1.10A1-207[»]
2F7NX-ray2.00A1-207[»]
ProteinModelPortaliQ9RS64.
SMRiQ9RS64. Positions 30-207.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243230.DR_2263.

Proteomic databases

PRIDEiQ9RS64.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAF11811; AAF11811; DR_2263.
GeneIDi1800263.
KEGGidra:DR_2263.
PATRICi21632226. VBIDeiRad64572_2491.

Phylogenomic databases

eggNOGiENOG4105IJD. Bacteria.
COG0783. LUCA.
HOGENOMiHOG000099528.
InParanoidiQ9RS64.
KOiK04047.
OMAiVWFLFES.
OrthoDBiEOG6Z9B6G.

Enzyme and pathway databases

BioCyciDRAD243230:GH46-2311-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9RS64.

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]
PRINTSiPR01346. HELNAPAPROT.
SUPFAMiSSF47240. SSF47240. 1 hit.
PROSITEiPS00818. DPS_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
  2. "Differential DNA binding and protection by dimeric and dodecameric forms of the ferritin homolog Dps from Deinococcus radiodurans."
    Grove A., Wilkinson S.P.
    J. Mol. Biol. 347:495-508(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: DNA-BINDING, FUNCTION IN DNA PROTECTION, SUBUNIT.
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.

Entry informationi

Entry nameiDPS1_DEIRA
AccessioniPrimary (citable) accession number: Q9RS64
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 17, 2006
Last sequence update: May 1, 2000
Last modified: November 11, 2015
This is version 103 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Dodecameric dps forms large aggregates upon binding to DNA.
Addition of Ca2+ to dodecameric dps can result in the reduction of bound Fe3+.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.