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Protein

DNA protection during starvation protein

Gene

dps

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

During stationary phase, binds the chromosome non-specifically, forming a highly ordered and stable dps-DNA co-crystal within which chromosomal DNA is condensed and protected from diverse damages. It protects DNA from oxidative damage by sequestering intracellular Fe2+ ion and storing it in the form of Fe3+ oxyhydroxide mineral, which can be released after reduction. One hydrogen peroxide oxidizes two Fe2+ ions, which prevents hydroxyl radical production by the Fenton reaction. Dps also protects the cell from UV and gamma irradiation, iron and copper toxicity, thermal stress and acid and base shocks. Also shows a weak catalase activity.4 Publications

Catalytic activityi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi51Iron 1; shared with dodecameric partner1
Metal bindingi78Iron 11
Metal bindingi82Iron 11
Metal bindingi82Iron 2Curated1

GO - Molecular functioni

  • DNA binding Source: EcoliWiki
  • ferric iron binding Source: EcoCyc
  • identical protein binding Source: IntAct
  • oxidoreductase activity, oxidizing metal ions Source: InterPro

GO - Biological processi

  • cellular iron ion homeostasis Source: UniProtKB-KW
  • chromosome condensation Source: UniProtKB-KW
  • response to starvation Source: EcoCyc

Keywordsi

Molecular functionDNA-binding, Oxidoreductase
Biological processDNA condensation, Iron storage
LigandIron, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11415-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
DNA protection during starvation protein (EC:1.16.-.-)
Gene namesi
Name:dps
Synonyms:pexB, vtm
Ordered Locus Names:b0812, JW0797
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11415 dps

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved4 Publications
ChainiPRO_00002016502 – 167DNA protection during starvation proteinAdd BLAST166

Proteomic databases

EPDiP0ABT2
PaxDbiP0ABT2
PRIDEiP0ABT2

2D gel databases

SWISS-2DPAGEiP0ABT2

Expressioni

Inductioni

Induced by RpoS and IHF in the early stationary phase. Induced by OxyR in response to oxidative stress during exponential phase. ClpXP probably directly regulate proteolysis of dps during exponential phase. ClpAP seems to play an indirect role in maintaining ongoing dps synthesis during stationary 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.2 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi4259973, 23 interactors
DIPiDIP-35919N
IntActiP0ABT2, 37 interactors
MINTiP0ABT2
STRINGi316385.ECDH10B_0880

Structurei

Secondary structure

1167
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni10 – 12Combined sources3
Helixi23 – 52Combined sources30
Helixi59 – 86Combined sources28
Helixi95 – 101Combined sources7
Helixi114 – 138Combined sources25
Helixi142 – 164Combined sources23

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DPSX-ray1.60A/B/C/D/E/F/G/H/I/J/K/L1-167[»]
1F30X-ray2.85A/B/C/D/E/F/G/H/I/J/K/L1-167[»]
1F33X-ray2.60A/B/C/D/E/F/G/H/I/J/K/L1-167[»]
1JREX-ray2.65A/B/C/D/E/F/G/H/I/J/K/L1-167[»]
1JTSX-ray2.60A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/W/X1-167[»]
1L8HX-ray3.20A/B/C/D/E/F/G/H/I/J/K/L1-167[»]
1L8IX-ray3.00A/B/C/D/E/F/G/H/I/J/K/L1-167[»]
2W9RX-ray1.70B6-16[»]
3O2HX-ray1.70B6-16[»]
5XGOX-ray1.99A/B/C/D/E/F/G/H/I/J/K/L1-163[»]
ProteinModelPortaliP0ABT2
SMRiP0ABT2
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0ABT2

Family & Domainsi

Domaini

12 dinuclear ferroxidase centers are located at the interfaces between subunits related by 2-fold symmetry axes. The lysine-rich N-terminus is required for self-aggregation as well as for dps-driven DNA condensation.

Sequence similaritiesi

Belongs to the Dps family.Curated

Phylogenomic databases

eggNOGiENOG4105DPV Bacteria
COG0783 LUCA
HOGENOMiHOG000273542
InParanoidiP0ABT2
KOiK04047
OMAiDDYSIGR
PhylomeDBiP0ABT2

Family and domain databases

CDDicd01043 DPS, 1 hit
Gene3Di1.20.1260.10, 1 hit
HAMAPiMF_01441 Dps, 1 hit
InterProiView protein in InterPro
IPR002177 DPS_DNA-bd
IPR023188 DPS_DNA-bd_CS
IPR023067 Dps_gammaproteobac
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
PS00819 DPS_2, 1 hit

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0ABT2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTAKLVKSK ATNLLYTRND VSDSEKKATV ELLNRQVIQF IDLSLITKQA
60 70 80 90 100
HWNMRGANFI AVHEMLDGFR TALIDHLDTM AERAVQLGGV ALGTTQVINS
110 120 130 140 150
KTPLKSYPLD IHNVQDHLKE LADRYAIVAN DVRKAIGEAK DDDTADILTA
160
ASRDLDKFLW FIESNIE
Length:167
Mass (Da):18,695
Last modified:January 23, 2007 - v2
Checksum:i596A79B1C6A5E60B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti18R → N AA sequence (PubMed:7984106).Curated1
Sequence conflicti68G → A in AAA21855 (PubMed:8021175).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X69337 Genomic DNA Translation: CAA49169.1
U04242 Genomic DNA Translation: AAA21855.1
U00096 Genomic DNA Translation: AAC73899.1
AP009048 Genomic DNA Translation: BAA35484.1
X14180 Genomic DNA No translation available.
PIRiA46401
RefSeqiNP_415333.1, NC_000913.3
WP_000100800.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC73899; AAC73899; b0812
BAA35484; BAA35484; BAA35484
GeneIDi945101
KEGGiecj:JW0797
eco:b0812
PATRICifig|1411691.4.peg.1466

Similar proteinsi

Entry informationi

Entry nameiDPS_ECOLI
AccessioniPrimary (citable) accession number: P0ABT2
Secondary accession number(s): P27430
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 25, 2005
Last sequence update: January 23, 2007
Last modified: April 25, 2018
This is version 117 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome
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Main funding by: National Institutes of Health