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Protein

DNA protection during starvation protein

Gene

dps

Organism
Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halobacterium halobium)
Status
Reviewed-Annotation score: Annotation score: 4 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. One hydrogen peroxide oxidizes two Fe2+ ions, which prevents hydroxyl radical production by the Fenton reaction (By similarity).By similarity

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi52 – 521Iron 1; shared with dodecameric partner1 Publication
Sitei53 – 531Involved in iron translocation
Sitei56 – 561Involved in iron translocation
Sitei75 – 751Involved in iron nucleation
Metal bindingi79 – 791Iron 11 Publication
Metal bindingi83 – 831Iron 11 Publication
Metal bindingi83 – 831Iron 2Sequence analysis
Sitei85 – 851Involved in iron translocation
Sitei86 – 861Involved in iron translocation
Sitei154 – 1541Involved in iron nucleation
Sitei164 – 1641Involved in iron translocation
Sitei168 – 1681Involved in iron translocation
Sitei171 – 1711Involved in iron translocation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Iron storage

Keywords - Ligandi

Iron, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA protection during starvation protein (EC:1.16.-.-)
Alternative name(s):
Bacterioferritin DpsA
Gene namesi
Name:dps
Synonyms:dpsA
Ordered Locus Names:VNG_2443G
ORF Names:OE4427R
OrganismiHalobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) (Halobacterium halobium)
Taxonomic identifieri64091 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaHalobacteriaHalobacterialesHalobacteriaceaeHalobacterium
Proteomesi
  • UP000000554 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 182182DNA protection during starvation proteinPRO_0000201656Add
BLAST

Post-translational modificationi

The N-terminus is blocked.

Proteomic databases

PaxDbiQ9HMP7.
PRIDEiQ9HMP7.

Interactioni

Subunit structurei

Homododecamer. The 12 subunits form a hollow sphere into which the mineral iron core of up to 110 Fe3+ can be deposited.1 Publication

Protein-protein interaction databases

STRINGi64091.VNG2443G.

Structurei

Secondary structure

1
182
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni18 – 214Combined sources
Helixi24 – 5431Combined sources
Helixi60 – 8728Combined sources
Helixi96 – 1027Combined sources
Beta strandi110 – 1123Combined sources
Helixi115 – 14228Combined sources
Helixi146 – 16924Combined sources
Turni178 – 1803Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1MOJX-ray1.90A/B/C/D1-182[»]
1TJOX-ray1.60A/B/C/D1-182[»]
1TK6X-ray2.20A/B/C/D1-182[»]
1TKOX-ray2.90A/B/C/D1-182[»]
1TKPX-ray2.20A/B/C/D1-182[»]
ProteinModelPortaliQ9HMP7.
SMRiQ9HMP7. Positions 2-181.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9HMP7.

Family & Domainsi

Sequence similaritiesi

Belongs to the Dps family.Curated

Phylogenomic databases

eggNOGiarCOG01101. Archaea.
COG0783. LUCA.
InParanoidiQ9HMP7.
OMAiVWFLFES.
PhylomeDBiQ9HMP7.

Family and domain databases

Gene3Di1.20.1260.10. 1 hit.
InterProiIPR002177. DPS_DNA-bd.
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.

Sequencei

Sequence statusi: Complete.

Q9HMP7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTQKNARAT AGEVEGSDAL RMDADRAEQC VDALNADLAN VYVLYHQLKK
60 70 80 90 100
HHWNVEGAEF RDLHLFLGEA AETAEEVADE LAERVQALGG VPHASPETLQ
110 120 130 140 150
AEASVDVEDE DVYDIRTSLA NDMAIYGDII EATREHTELA ENLGDHATAH
160 170 180
MLREGLIELE DDAHHIEHYL EDDTLVTQGA LE
Length:182
Mass (Da):20,100
Last modified:March 1, 2001 - v1
Checksum:iBC1EA5E7C5F61636
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE004437 Genomic DNA. Translation: AAG20524.1.
PIRiH84394.
RefSeqiWP_010903826.1. NC_002607.1.

Genome annotation databases

EnsemblBacteriaiAAG20524; AAG20524; VNG_2443G.
GeneIDi5953388.
KEGGihal:VNG2443G.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE004437 Genomic DNA. Translation: AAG20524.1.
PIRiH84394.
RefSeqiWP_010903826.1. NC_002607.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1MOJX-ray1.90A/B/C/D1-182[»]
1TJOX-ray1.60A/B/C/D1-182[»]
1TK6X-ray2.20A/B/C/D1-182[»]
1TKOX-ray2.90A/B/C/D1-182[»]
1TKPX-ray2.20A/B/C/D1-182[»]
ProteinModelPortaliQ9HMP7.
SMRiQ9HMP7. Positions 2-181.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi64091.VNG2443G.

Proteomic databases

PaxDbiQ9HMP7.
PRIDEiQ9HMP7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAG20524; AAG20524; VNG_2443G.
GeneIDi5953388.
KEGGihal:VNG2443G.

Phylogenomic databases

eggNOGiarCOG01101. Archaea.
COG0783. LUCA.
InParanoidiQ9HMP7.
OMAiVWFLFES.
PhylomeDBiQ9HMP7.

Miscellaneous databases

EvolutionaryTraceiQ9HMP7.

Family and domain databases

Gene3Di1.20.1260.10. 1 hit.
InterProiIPR002177. DPS_DNA-bd.
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.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Oesterhelt D., Pfeiffer F.
    Unpublished observations (NOV-2001)
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700922 / JCM 11081 / NRC-1.
  3. "The DpsA-homologue of the archaeon Halobacterium salinarum is a ferritin."
    Reindel S., Anemueller S., Sawaryn A., Matzanke B.F.
    Biochim. Biophys. Acta 1598:140-146(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 23-37, CIRCULAR DICHROISM ANALYSIS, PARTIAL CHARACTERIZATION.
    Strain: ATCC 33171 / DSM 3754 / JCM 8978 / NCIMB 764 / NRC 34002.
  4. "Iron-oxo clusters biomineralizing on protein surfaces: structural analysis of Halobacterium salinarum DpsA in its low- and high-iron states."
    Zeth K., Offermann S., Essen L.-O., Oesterhelt D.
    Proc. Natl. Acad. Sci. U.S.A. 101:13780-13785(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF N-TERMINUS, X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH IRON, SUBUNIT.

Entry informationi

Entry nameiDPS_HALSA
AccessioniPrimary (citable) accession number: Q9HMP7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2003
Last sequence update: March 1, 2001
Last modified: December 9, 2015
This is version 100 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The dps dodecamer comprises iron-binding sites for iron translocation, oxidation and nucleation. Fe2+ atoms are initially bound to the outer surface in proximity to the iron entry pore from which they are translocated toward the inter-subunit ferroxidase centers via two discrete steps. Iron oxidation proceeds by transient formation of tri-iron ferroxidase centers and Fe3+ atoms move to two distinct iron nucleation centers where iron mineralization occurs.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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.