dps:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

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Standard Name

dps

Gene Synonym(s)

ECK0801, b0812, JW0797, pexB, vtm[1], vtm

Product Desc.

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]

Product Synonyms(s)

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

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): dps[2], OP00242

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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dps is required for growth below 8C, which is enabled by transgenic Oleispira antarctica Cpn10/60.[4]



Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

dps

Mnemonic

DNA-binding Protein from Starved cells

Synonyms

ECK0801, b0812, JW0797, pexB, vtm[1], vtm

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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

18.27 minutes 

MG1655: 848134..847631
<gbrowseImage> name=NC_000913:847631..848134 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 841536..841033
<gbrowseImage> name=NC_012967:841033..841536 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 750599..751102
<gbrowseImage> name=NC_012759:750599..751102 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 849333..848830
<gbrowseImage> name=NC_007779:848830..849333 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 902062..901559
<gbrowseImage> name=NC_010473:901559..902062 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

847634

Edman degradation

PMID:7984106
PMID:8354462
PMID:9298646


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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

Δdps (Keio:JW0797)

deletion

deletion

PMID:16738554

Shigen
CGSC8844[5]

dps::Tn5KAN-2 (FB20241)

Insertion at nt 212 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20241

does not contain pKD46

Δdps-784::kan

PMID:16738554

CGSC:100646


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW0797

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGTACCGCTAAATTAGTTAA

Primer 2:CCTTCGATGTTAGACTCGATAAA

10A8

Kohara Phage

Genobase

PMID:3038334

4C6

Kohara Phage

Genobase

PMID:3038334

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[5]

est. P1 cotransduction: 37% [6]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[5]

est. P1 cotransduction: % [6]
Synonyms:zbj-1230::Tn10

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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

EcoCyc

EcoCyc:EG11415

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11415

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001381

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945101

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1387

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002776

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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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

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

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

Experiment(s):EBI-885194

Protein

hrpA

PMID:15690043

Experiment(s):EBI-885194

Protein

lon

PMID:15690043

Experiment(s):EBI-885194

Protein

ompG

PMID:15690043

Experiment(s):EBI-885194

Protein

hldD

PMID:15690043

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

Protein

tpx

PMID:16606699

Experiment(s):EBI-1138083

Protein

hfq

PMID:15690043

Experiment(s):EBI-891956

Protein

skp

PMID:15690043

Experiment(s):EBI-891956

Protein

rplW

PMID:15690043

Experiment(s):EBI-891956

Protein

rplX

PMID:15690043

Experiment(s):EBI-891956

Protein

rpsE

PMID:15690043

Experiment(s):EBI-891956

Protein

rpsF

PMID:15690043

Experiment(s):EBI-891956

Protein

rpsH

PMID:15690043

Experiment(s):EBI-891956

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-891956

Protein

slyD

PMID:15690043

Experiment(s):EBI-891956

Protein

yibL

PMID:15690043

Experiment(s):EBI-891956

Protein

rfaD

PMID:19402753

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

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

slyD

PMID:19402753

LCMS(ID Probability):99.6

Protein

yibL

PMID:19402753

LCMS(ID Probability):99.6

Protein

dnaN

PMID:19402753

MALDI(Z-score):38.391290

Protein

rpsM

PMID:19402753

MALDI(Z-score):17.675492

Protein

rpsH

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsJ

PMID:19402753

LCMS(ID Probability):99.6

Protein

skp

PMID:19402753

LCMS(ID Probability):99.6

Protein

deaD

PMID:19402753

MALDI(Z-score):22.861392

Protein

rplW

PMID:19402753

LCMS(ID Probability):99.4

Protein

tig

PMID:19402753

MALDI(Z-score):36.383889

Protein

rpsA

PMID:19402753

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

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

Domain

30..167

PF00210 Ferritin-like domain

PMID:19920124

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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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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

3.73E+03

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

Ecoli K-12

8.687+/-0.074

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

3.314115308

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

2131

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

13008

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

2446

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

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

Transcription unit(s)

dps

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Figure courtesy of RegulonDB

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:848114..848154 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b0812 (EcoliWiki Page)

NCBI GEO profiles for dps

microarray

GenExpDB:b0812 (EcoliWiki Page)

Summary of data for dps from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (848065..848483) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ02; Well:B12[7]

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Notes

Accessions Related to dps Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11415

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1387

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0812

EcoGene

EcoGene:EG11415

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001381

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002776

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Evolution

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Homologs in Other Organisms

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

Organism Homologs (Statistics) Comments

Xenopus tropicalis

  • ENSXETP00000043411 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

DPS

From SHIGELLACYC

E. coli O157

DPS

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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

Database Accession Notes

Pfam (EcoliWiki Page)

PF00210 Ferritin-like domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:47240

EcoCyc

EcoCyc:EG11415

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11415

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

ASAP

ASAP:ABE-0002776

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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 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 3.3 3.4 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
  7. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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