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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: -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

Miscellaneous

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

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

Keywordsi

Molecular functionDNA-binding, Oxidoreductase
Biological processIron storage
LigandIron, 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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002533261 – 207DNA protection during starvation protein 1Add BLAST207

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

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
OMAiTLYLQTH
OrthoDBiPOG091H00MO

Family and domain databases

CDDicd01043 DPS, 1 hit
Gene3Di1.20.1260.10, 1 hit
InterProiView protein in InterPro
IPR002177 DPS_DNA-bd
IPR023188 DPS_DNA-bd_CS
IPR012347 Ferritin-like
IPR009078 Ferritin-like_SF
IPR008331 Ferritin_DPS_dom
PANTHERiPTHR42932 PTHR42932, 1 hit
PfamiView protein in Pfam
PF00210 Ferritin, 1 hit
PIRSFiPIRSF005900 Dps, 1 hit
PRINTSiPR01346 HELNAPAPROT
SUPFAMiSSF47240 SSF47240, 1 hit
PROSITEiView protein in PROSITE
PS00818 DPS_1, 1 hit

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
PATRICifig|243230.17.peg.2491

Similar proteinsi

Entry informationi

Entry nameiDPS1_DEIRA
AccessioniPrimary (citable) accession number: Q9RS64
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 17, 2006
Last sequence update: May 1, 2000
Last modified: May 23, 2018
This is version 110 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

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

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