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Protein

DNA protection during starvation protein

Gene

dps

Organism
Mycobacterium smegmatis
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). It protects DNA from hydroxyl radical-mediated cleavage. Binds DNA with no apparent sequence specificity without self-aggregation nor promotion of DNA condensation. Is unable to protect DNA from DNase-mediated cleavage.By similarity1 Publication

Caution

The sequence shown here has been extracted from PDB entry 1UVH.Curated

Catalytic activityi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi39Iron 1; shared with dodecameric partner2 Publications1
Metal bindingi66Iron 12 Publications1
Metal bindingi70Iron 12 Publications1
Metal bindingi70Iron 22 Publications1

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 (EC:1.16.-.-)
Gene namesi
Name:dps
OrganismiMycobacterium smegmatis
Taxonomic identifieri1772 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium fortuitum complex

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002533331 – 183DNA protection during starvation proteinAdd BLAST183

Interactioni

Subunit structurei

The 12 identical subunits form a hollow sphere into which the mineral iron core of up to 500 Fe3+ can be deposited (By similarity). Homododecamer.By similarity3 Publications

Structurei

Secondary structure

1183
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi14 – 41Combined sources28
Beta strandi42 – 44Combined sources3
Helixi47 – 74Combined sources28
Helixi83 – 89Combined sources7
Beta strandi99 – 101Combined sources3
Helixi102 – 127Combined sources26
Turni128 – 130Combined sources3
Helixi132 – 156Combined sources25
Beta strandi159 – 161Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UVHX-ray2.80A/B/C/D1-183[»]
1VEIX-ray2.85A1-183[»]
1VELX-ray2.99A/B/C/D/E/F1-183[»]
1VEQX-ray3.98A/B/C/D/E/F/G/H/I/J/K/L1-183[»]
2YW6X-ray2.53A/B/C1-183[»]
2YW7X-ray3.30A/B/C/D/E/F/G/H/I/J1-183[»]
ProteinModelPortaliP0C558
SMRiP0C558
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0C558

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

eggNOGiENOG4105DPV Bacteria
COG0783 LUCA

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.

P0C558-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTSFTIPGLS DKKASDVADL LQKQLSTYND LHLTLKHVHW NVVGPNFIGV
60 70 80 90 100
HEMIDPQVEL VRGYADEVAE RIATLGKSPK GTPGAIIKDR TWDDYSVERD
110 120 130 140 150
TVQAHLAALD LVYNGVIEDT RKSIEKLEDL DLVSQDLLIA HAGELEKFQW
160 170 180
FVRAHLESAG GQLTHEGQST EKGAADKARR KSA
Length:183
Mass (Da):20,270
Last modified:July 10, 2007 - v1
Checksum:i3ACB34B43B23F877
GO

Sequence databases

RefSeqiWP_003897878.1, NZ_LN831039.1

Similar proteinsi

Entry informationi

Entry nameiDPS_MYCSM
AccessioniPrimary (citable) accession number: P0C558
Secondary accession number(s): Q8VP75
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 10, 2007
Last sequence update: July 10, 2007
Last modified: May 23, 2018
This is version 49 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

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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