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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)DescriptionActionsGraphical viewLength
Metal bindingi83Iron 1; shared with dodecameric partnerBy similarity1
Metal bindingi110Iron 1By similarity1
Metal bindingi114Iron 1By similarity1
Metal bindingi114Iron 2By similarity1

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

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)DescriptionActionsGraphical viewLength
ChainiPRO_00002533261 – 207DNA protection during starvation protein 1Add BLAST207

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

1207
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi33 – 35Combined sources3
Helixi55 – 85Combined sources31
Helixi91 – 105Combined sources15
Helixi108 – 118Combined sources11
Helixi127 – 133Combined sources7
Helixi146 – 173Combined sources28
Helixi177 – 201Combined sources25

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2C2FX-ray1.61A1-207[»]
2C2UX-ray1.10A1-207[»]
2F7NX-ray2.00A1-207[»]
ProteinModelPortaliQ9RS64.
SMRiQ9RS64.
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.
OrthoDBiPOG091H00MO.

Family and domain databases

CDDicd01043. DPS. 1 hit.
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. NZ_CP015081.1.

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. NZ_CP015081.1.

3D structure databases

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

Protein-protein interaction databases

STRINGi243230.DR_2263.

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.
OrthoDBiPOG091H00MO.

Miscellaneous databases

EvolutionaryTraceiQ9RS64.

Family and domain databases

CDDicd01043. DPS. 1 hit.
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...

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 2, 2016
This is version 106 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.