dps:Gene Product(s)

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Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

Dps

Synonyms

Fe-binding and storage protein[1], B0812[2][1], Vtm[2][1], PexB[2][1], Dps[2][1] , ECK0801, JW0797, pexB, vtm, b0812

Product description

stationary phase nucleoid protein that sequesters iron and protects DNA from damage[2][3];

Component of Dps complex; stationary phase nucleoid component that sequesters iron and protects DNA from damage[3]

Stress response DNA-binding protein; starvation-induced resistance to H2O2; Fe-binding and storage protein; forms biocrystals with DNA[4]

EC number (for enzymes)


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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
GO:0003677

DNA binding

PMID:10551881[5]

IDA: Inferred from Direct Assay

F

complete

GO:0003677

DNA binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01441

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0005506

iron ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0408

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01441

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0006879

cellular iron ion homeostasis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008331

P

Seeded from EcoCyc (v14.0)

complete

GO:0006879

cellular iron ion homeostasis

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0409

P

Seeded from EcoCyc (v14.0)

complete

GO:0006950

response to stress

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002177

P

Seeded from EcoCyc (v14.0)

complete

GO:0008199

ferric iron binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01441

F

Seeded from EcoCyc (v14.0)

complete

GO:0008199

ferric iron binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR008331

F

Seeded from EcoCyc (v14.0)

complete

GO:0009295

nucleoid

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0187

C

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

PMID:16858726[6]

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01441

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009078

F

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0046914

transition metal ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009078

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002177

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009078

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

P

Seeded from EcoCyc (v14.0)

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

Subunits of Dps complex; stationary phase nucleoid component that sequesters iron and protects DNA from damage

could be indirect

Protein

deaD

PMID:15690043[7]

Experiment(s):EBI-885194

Protein

hrpA

PMID:15690043[7]

Experiment(s):EBI-885194

Protein

lon

PMID:15690043[7]

Experiment(s):EBI-885194

Protein

ompG

PMID:15690043[7]

Experiment(s):EBI-885194

Protein

hldD

PMID:15690043[7]

Experiment(s):EBI-885194, EBI-891956

Protein

tpx

PMID:16606699[8]

Experiment(s):EBI-1138083

Protein

hfq

PMID:15690043[7]

Experiment(s):EBI-891956

Protein

skp

PMID:15690043[7]

Experiment(s):EBI-891956

Protein

rplW

PMID:15690043[7]

Experiment(s):EBI-891956

Protein

rplX

PMID:15690043[7]

Experiment(s):EBI-891956

Protein

rpsE

PMID:15690043[7]

Experiment(s):EBI-891956

Protein

rpsF

PMID:15690043[7]

Experiment(s):EBI-891956

Protein

rpsH

PMID:15690043[7]

Experiment(s):EBI-891956

Protein

rpsJ

PMID:15690043[7]

Experiment(s):EBI-891956

Protein

slyD

PMID:15690043[7]

Experiment(s):EBI-891956

Protein

yibL

PMID:15690043[7]

Experiment(s):EBI-891956

Protein

rfaD

PMID:19402753[9]

LCMS(ID Probability):99.6 MALDI(Z-score):39.501924

Protein

rpsF

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

slyD

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

yibL

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

dnaN

PMID:19402753[9]

MALDI(Z-score):38.391290

Protein

rpsM

PMID:19402753[9]

MALDI(Z-score):17.675492

Protein

rpsH

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

rpsJ

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

skp

PMID:19402753[9]

LCMS(ID Probability):99.6

Protein

deaD

PMID:19402753[9]

MALDI(Z-score):22.861392

Protein

rplW

PMID:19402753[9]

LCMS(ID Probability):99.4

Protein

tig

PMID:19402753[9]

MALDI(Z-score):36.383889

Protein

rpsA

PMID:19402753[9]

MALDI(Z-score):19.670966

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes

cytoplasm

From EcoCyc[3]

Cytoplasm

PMID:7984106[10]

EchoLocation:dps


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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MSTAKLVKSK ATNLLYTRND VSDSEKKATV ELLNRQVIQF IDLSLITKQA HWNMRGANFI
AVHEMLDGFR TALIDHLDTM AERAVQLGGV ALGTTQVINS KTPLKSYPLD IHNVQDHLKE
LADRYAIVAN DVRKAIGEAK DDDTADILTA ASRDLDKFLW FIESNIE
Length

167

Mol. Wt

18.695 kDa

pI

6.1 (calculated)

Extinction coefficient

15,470 (calc based on 3 Y, 2 W, and 0 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Initiator Methionine

1

Removed

UniProt:P0ABT2

Modification Site

107

phosphorylation site at Y107

probability greater than 75%

PMID:17938405[11]

Domain

30..167

PF00210 Ferritin-like domain

PMID:19920124[12]

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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=dps taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16128780

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945101

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002776

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ABT2

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11415

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11415

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945101

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001381

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1387

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ Azam, TA & Ishihama, A (1999) Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J. Biol. Chem. 274 33105-13 PubMed
  6. ↑ Lasserre, JP et al. (2006) A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis. Electrophoresis 27 3306-21 PubMed
  7. ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 7.11 7.12 7.13 7.14 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  8. ↑ Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  9. ↑ 9.00 9.01 9.02 9.03 9.04 9.05 9.06 9.07 9.08 9.09 9.10 9.11 9.12 9.13 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  10. ↑ Altuvia, S et al. (1994) The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase. Mol. Microbiol. 13 265-72 PubMed
  11. ↑ Macek, B et al. (2008) Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation. Mol. Cell Proteomics 7 299-307 PubMed
  12. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

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