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Protein

DNA protection during starvation protein

Gene

dps

Organism
Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens (strain C58))
Status
Reviewed-Annotation score: Annotation score: 3 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, which can be released after reduction. It efficiently inhibits hydroxyl radical production by the Fenton reaction. Does not bind DNA.1 Publication

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi40 – 401Iron1 Publication
Metal bindingi67 – 671IronBy similarity
Metal bindingi71 – 711Iron1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Iron storage

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciAGRO:ATU2477-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA protection during starvation protein (EC:1.16.-.-)
Gene namesi
Name:dps
Ordered Locus Names:Atu2477
ORF Names:AGR_C_4495
OrganismiAgrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens (strain C58))
Taxonomic identifieri176299 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeRhizobium/Agrobacterium groupAgrobacteriumAgrobacterium tumefaciens complex
Proteomesi
  • UP000000813 Componenti: Chromosome circular

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Chemistry

DrugBankiDB03754. Tris.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 162162DNA protection during starvation proteinPRO_0000253329Add
BLAST

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.1 Publication

Protein-protein interaction databases

STRINGi176299.Atu2477.

Structurei

Secondary structure

1
162
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi12 – 4231Combined sources
Helixi48 – 7528Combined sources
Helixi84 – 907Combined sources
Helixi103 – 13028Combined sources
Helixi134 – 15623Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1O9RX-ray1.45A/B/C/D/E/F1-162[»]
ProteinModelPortaliQ8UCK6.
SMRiQ8UCK6. Positions 1-162.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8UCK6.

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.
HOGENOMiHOG000273542.
KOiK04047.
OrthoDBiEOG6Z9B6G.

Family and domain databases

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]
PIRSFiPIRSF005900. Dps. 1 hit.
PRINTSiPR01346. HELNAPAPROT.
SUPFAMiSSF47240. SSF47240. 1 hit.
PROSITEiPS00818. DPS_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8UCK6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKTHKTKNDL PSNAKSTVIG ILNESLASVI DLALVTKQAH WNLKGPQFIA
60 70 80 90 100
VHELLDTFRT QLDNHGDTIA ERVVQLGGTA LGSLQAVSST TKLKAYPTDI
110 120 130 140 150
YKIHDHLDAL IERYGEVANM IRKAIDDSDE AGDPTTADIF TAASRDLDKS
160
LWFLEAHVQE KS
Length:162
Mass (Da):17,823
Last modified:June 1, 2002 - v1
Checksum:i8C34BF85B570ED15
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE007869 Genomic DNA. Translation: AAK88212.1.
PIRiAC2881.
C97657.
RefSeqiNP_355427.1. NC_003062.2.
WP_006312098.1. NC_003062.2.

Genome annotation databases

EnsemblBacteriaiAAK88212; AAK88212; Atu2477.
GeneIDi1134515.
KEGGiatu:Atu2477.
PATRICi20814743. VBIAgrTum91616_2490.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE007869 Genomic DNA. Translation: AAK88212.1.
PIRiAC2881.
C97657.
RefSeqiNP_355427.1. NC_003062.2.
WP_006312098.1. NC_003062.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1O9RX-ray1.45A/B/C/D/E/F1-162[»]
ProteinModelPortaliQ8UCK6.
SMRiQ8UCK6. Positions 1-162.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi176299.Atu2477.

Chemistry

DrugBankiDB03754. Tris.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAK88212; AAK88212; Atu2477.
GeneIDi1134515.
KEGGiatu:Atu2477.
PATRICi20814743. VBIAgrTum91616_2490.

Phylogenomic databases

eggNOGiENOG4105DPV. Bacteria.
COG0783. LUCA.
HOGENOMiHOG000273542.
KOiK04047.
OrthoDBiEOG6Z9B6G.

Enzyme and pathway databases

BioCyciAGRO:ATU2477-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ8UCK6.

Family and domain databases

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]
PIRSFiPIRSF005900. Dps. 1 hit.
PRINTSiPR01346. HELNAPAPROT.
SUPFAMiSSF47240. SSF47240. 1 hit.
PROSITEiPS00818. DPS_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C58 / ATCC 33970.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C58 / ATCC 33970.
  3. "The Dps protein of Agrobacterium tumefaciens does not bind to DNA but protects it toward oxidative cleavage: X-ray crystal structure, iron binding, and hydroxyl-radical scavenging properties."
    Ceci P., Ilari A., Falvo E., Chiancone E.
    J. Biol. Chem. 278:20319-20326(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) IN COMPLEX WITH IRON, FUNCTION IN DNA PROTECTION, SUBUNIT.
    Strain: GV3101.

Entry informationi

Entry nameiDPS_AGRFC
AccessioniPrimary (citable) accession number: Q8UCK6
Secondary accession number(s): Q7CWY8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 17, 2006
Last sequence update: June 1, 2002
Last modified: December 9, 2015
This is version 88 of the entry and version 1 of the sequence. [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

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.