DNA protection during starvation protein - Listeria innocua serovar 6a (strain CLIP 11262)

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P80725 (DPS_LISIN) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 101. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
DNA protection during starvation protein
EC=1.16.-.-

Alternative name(s):
Ferritin-like protein
Non-heme iron-containing ferritin

Gene names

Name:	dps
Synonyms:	flp, fri
Ordered Locus Names:	lin0942

Organism

Listeria innocua serovar 6a (strain CLIP 11262) [Complete proteome] [HAMAP]

Taxonomic identifier

272626 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacilli › Bacillales › Listeriaceae › Listeria ›

Protein attributes

Sequence length	156 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Does not bind DNA. Ref.1 Ref.2 Ref.4
Catalytic activity	2 Fe²⁺ + H₂O₂ + 2 H⁺ = 2 Fe³⁺ + 2 H₂O.
Subunit structure	Homododecamer. The 12 subunits form a hollow sphere into which the mineral iron core of up to 500 Fe³⁺ can be deposited. Ref.5
Subcellular location	Cytoplasm By similarity.
Induction	By iron limitation and stationary growth phase. Ref.2
Domain	12 di-nuclear ferroxidase centers are located at the interfaces between subunits related by 2-fold symmetry axes.
Sequence similarities	Belongs to the dps family.

Ontologies

Keywords
Biological process	Iron storage
Cellular component	Cytoplasm
Ligand	Iron Metal-binding
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological_process	cellular iron ion homeostasis Inferred from electronic annotation. Source: UniProtKB-KW response to stress Inferred from electronic annotation. Source: InterPro
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ferric iron binding Inferred from electronic annotation. Source: InterPro oxidoreductase activity, oxidizing metal ions Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 156

156

DNA protection during starvation protein

PRO_0000201657

Sites

Metal binding

Iron 1; shared with dodecameric partner

Metal binding

Iron 1

Metal binding

Iron 1

Metal binding

Iron 2 Probable

Experimental info

Mutagenesis

H → G: Slight decrease in DNA protection and significant decrease in iron affinity. Retains only one third of wild-type DNA protection and loses iron binding ability; when associated with G-43. Ref.6

Mutagenesis

H → G: Slight decrease in DNA protection and significant decrease iron affinity. Retains only one third of wild-type DNA protection and loses iron-binding ability; when associated with G-31. Ref.6

Sequence conflict

R → L Ref.2

Secondary structure

156

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P80725 [UniParc].

Last modified November 1, 1997. Version 1.
Checksum: 5FC9FFF5EE7FB6F8
Show »

FASTA

156

18,049

        10         20         30         40         50         60 
MKTINSVDTK EFLNHQVANL NVFTVKIHQI HWYMRGHNFF TLHEKMDDLY SEFGEQMDEV 

        70         80         90        100        110        120 
AERLLAIGGS PFSTLKEFLE NASVEEAPYT KPKTMDQLME DLVGTLELLR DEYKQGIELT 

       130        140        150 
DKEGDDVTND MLIAFKASID KHIWMFKAFL GKAPLE

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A novel non-heme iron-binding ferritin related to the DNA-binding proteins of the Dps family in Listeria innocua." Bozzi M., Mignogna G., Stefanini S., Barra D., Longhi C., Valenti P., Chiancone E. J. Biol. Chem. 272:3259-3265(1997) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE, FUNCTION.
[2]	"The expression of the dodecameric ferritin in Listeria spp. is induced by iron limitation and stationary growth phase." Polidoro M., De Biase D., Montagnini B., Guarrera L., Cavallo S., Valenti P., Stefanini S., Chiancone E. Gene 296:121-128(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, INDUCTION. Strain: LS1.
[3]	"Comparative genomics of Listeria species." Glaser P., Frangeul L., Buchrieser C., Rusniok C., Amend A., Baquero F., Berche P., Bloecker H., Brandt P., Chakraborty T., Charbit A., Chetouani F., Couve E., de Daruvar A., Dehoux P., Domann E., Dominguez-Bernal G., Duchaud E. Cossart P. Science 294:849-852(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: CLIP 11262.
[4]	"The so-called Listeria innocua ferritin is a Dps protein. Iron incorporation, detoxification, and DNA protection properties." Su M., Cavallo S., Stefanini S., Chiancone E., Chasteen N.D. Biochemistry 44:5572-5578(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION IN DNA PROTECTION, IRON INCORPORATION.
[5]	"The dodecameric ferritin from Listeria innocua contains a novel intersubunit iron-binding site." Ilari A., Stefanini S., Chiancone E., Tsernoglou D. Nat. Struct. Biol. 7:38-43(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEX WITH IRON, SUBUNIT.
[6]	"The unusual intersubunit ferroxidase center of Listeria innocua Dps is required for hydrogen peroxide detoxification but not for iron uptake. A study with site-specific mutants." Ilari A., Latella M.C., Ceci P., Ribacchi F., Su M., Giangiacomo L., Stefanini S., Chasteen N.D., Chiancone E. Biochemistry 44:5579-5587(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.19 ANGSTROMS) OF MUTANTS GLY-31 AND GLY-43, MUTAGENESIS OF HIS-31 AND HIS-43.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AJ244014 Genomic DNA. Translation: CAB65175.2.
AL596167 Genomic DNA. Translation: CAC96173.1.

PIR

AE1550.

RefSeq

NP_470279.1. NC_003212.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1QGH	X-ray	2.35	A/B/C/D/E/F/G/H/I/J/K/L	1-156	[»]
2BJY	X-ray	2.60	A/B/C/D/E/F/G/H/I/J/K/L	1-156	[»]
2BK6	X-ray	2.19	A/B/C/D/E/F	1-156	[»]
2BKC	X-ray	2.30	A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T/U/V/X/Y	1-156	[»]

ProteinModelPortal

P80725.

SMR

P80725. Positions 7-156.

ModBase

Search...

Protein-protein interaction databases

STRING

272626.lin0942.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

CAC96173; CAC96173; CAC96173.

GeneID

1129452.

KEGG

lin:lin0942.

PATRIC

20298599. VBILisInn102668_0967.

Organism-specific databases

GenoList

LIN0942.

CMR

Search...

Phylogenomic databases

eggNOG

COG0783.

HOGENOM

HOG000273542.

K04047.

OMA

LMSDYIS.

ProtClustDB

CLSK564177.

Family and domain databases

Gene3D

1.20.1260.10. 1 hit.

InterPro

IPR002177. DPS_DNA-bd.
IPR023188. DPS_DNA-bd_CS.
IPR009078. Ferritin-like_SF.
IPR012347. Ferritin-rel.
IPR008331. Ferritin_DPS_dom.
[Graphical view]

Pfam

PF00210. Ferritin. 1 hit.
[Graphical view]

PIRSF

PIRSF005900. Dps. 1 hit.

PRINTS

PR01346. HELNAPAPROT.

SUPFAM

SSF47240. Ferritin/RR_like. 1 hit.

PROSITE

PS00818. DPS_1. 1 hit.
PS00819. DPS_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P80725.

Entry information

Entry name

DPS_LISIN

Accession

Primary (citable) accession number: P80725
Secondary accession number(s): Q9RE06

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	November 1, 1997
Last modified:	May 1, 2013
This is version 101 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Family and domain databases

Other

Entry information

Relevant documents