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Protein

DNA protection during starvation protein

Gene

dps

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi51 – 511Iron 1; shared with dodecameric partner
Metal bindingi78 – 781Iron 1
Metal bindingi82 – 821Iron 1
Metal bindingi82 – 821Iron 2Curated

GO - Molecular functioni

  • DNA binding Source: EcoliWiki
  • ferric iron binding Source: UniProtKB-HAMAP
  • 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
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA condensation, Iron storage

Keywords - Ligandi

DNA-binding, Iron, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11415-MONOMER.
ECOL316407:JW0797-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11415. dps.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-HAMAP
  • membrane Source: UniProtKB
  • nucleoid Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved4 Publications
Chaini2 – 167166DNA protection during starvation proteinPRO_0000201650Add
BLAST

Proteomic databases

EPDiP0ABT2.
PaxDbiP0ABT2.
PRIDEiP0ABT2.

2D gel databases

SWISS-2DPAGEP0ABT2.

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

WithEntry#Exp.IntActNotes
clpSP0A8Q65EBI-549640,EBI-561456
dnaAP030042EBI-549640,EBI-548951

Protein-protein interaction databases

BioGridi4259973. 6 interactions.
DIPiDIP-35919N.
IntActiP0ABT2. 31 interactions.
MINTiMINT-1220368.
STRINGi511145.b0812.

Structurei

Secondary structure

1
167
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni10 – 123Combined sources
Helixi23 – 5230Combined sources
Helixi59 – 8628Combined sources
Helixi95 – 1017Combined sources
Helixi114 – 13825Combined sources
Helixi142 – 16423Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliP0ABT2.
SMRiP0ABT2. Positions 9-167.
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.
OMAiDIHSVQD.
PhylomeDBiP0ABT2.

Family and domain databases

Gene3Di1.20.1260.10. 1 hit.
HAMAPiMF_01441. Dps. 1 hit.
InterProiIPR002177. DPS_DNA-bd.
IPR023188. DPS_DNA-bd_CS.
IPR023067. Dps_gammaproteobac.
IPR009078. Ferritin-like_SF.
IPR012347. Ferritin-rel.
IPR008331. Ferritin_DPS_dom.
[Graphical view]
PfamiPF00210. Ferritin. 1 hit.
[Graphical view]
PIRSFiPIRSF005900. Dps. 1 hit.
PRINTSiPR01346. HELNAPAPROT.
SUPFAMiSSF47240. SSF47240. 1 hit.
PROSITEiPS00818. DPS_1. 1 hit.
PS00819. DPS_2. 1 hit.
[Graphical view]

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti18 – 181R → N AA sequence (PubMed:7984106).Curated
Sequence conflicti68 – 681G → A in AAA21855 (PubMed:8021175).Curated

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.
PATRICi32116827. VBIEscCol129921_0839.

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliP0ABT2.
SMRiP0ABT2. Positions 9-167.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259973. 6 interactions.
DIPiDIP-35919N.
IntActiP0ABT2. 31 interactions.
MINTiMINT-1220368.
STRINGi511145.b0812.

2D gel databases

SWISS-2DPAGEP0ABT2.

Proteomic databases

EPDiP0ABT2.
PaxDbiP0ABT2.
PRIDEiP0ABT2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73899; AAC73899; b0812.
BAA35484; BAA35484; BAA35484.
GeneIDi945101.
KEGGiecj:JW0797.
eco:b0812.
PATRICi32116827. VBIEscCol129921_0839.

Organism-specific databases

EchoBASEiEB1387.
EcoGeneiEG11415. dps.

Phylogenomic databases

eggNOGiENOG4105DPV. Bacteria.
COG0783. LUCA.
HOGENOMiHOG000273542.
InParanoidiP0ABT2.
KOiK04047.
OMAiDIHSVQD.
PhylomeDBiP0ABT2.

Enzyme and pathway databases

BioCyciEcoCyc:EG11415-MONOMER.
ECOL316407:JW0797-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0ABT2.
PROiP0ABT2.

Family and domain databases

Gene3Di1.20.1260.10. 1 hit.
HAMAPiMF_01441. Dps. 1 hit.
InterProiIPR002177. DPS_DNA-bd.
IPR023188. DPS_DNA-bd_CS.
IPR023067. Dps_gammaproteobac.
IPR009078. Ferritin-like_SF.
IPR012347. Ferritin-rel.
IPR008331. Ferritin_DPS_dom.
[Graphical view]
PfamiPF00210. Ferritin. 1 hit.
[Graphical view]
PIRSFiPIRSF005900. Dps. 1 hit.
PRINTSiPR01346. HELNAPAPROT.
SUPFAMiSSF47240. SSF47240. 1 hit.
PROSITEiPS00818. DPS_1. 1 hit.
PS00819. DPS_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDPS_ECOLI
AccessioniPrimary (citable) accession number: P0ABT2
Secondary accession number(s): P27430
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 25, 2005
Last sequence update: January 23, 2007
Last modified: September 7, 2016
This is version 103 of the entry and version 2 of the sequence. [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

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.