RegulonDB RegulonDB 10.9: Gene Form
   

dps gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

rhtA glnH dps IHF OxyR OxyR Fis OxyR MntR Fis H-NS IHF NtrC NtrC NtrC NtrC IHF anti-anti-terminator anti-terminator terminator dpsp dpsp TSS_972 (cluster) TSS_972 (cluster) TSS_971 TSS_971 glnHp1 glnHp1 glnHp2 glnHp2

Gene      
Name: dps    Texpresso search in the literature
Synonym(s): ECK0801, EG11415, b0812, pexB, vtm
Genome position(nucleotides): 848408 <-- 848911 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.01
Reference(s): [1] Grainger DC., et al., 2008
External database links:  
ASAP:
 ABE-0002776
CGSC:
 31650
ECHOBASE:
 EB1387
ECOLIHUB:
 dps
OU-MICROARRAY:
 b0812
STRING:
 511145.b0812
COLOMBOS: dps


Product      
Name: DNA protection during starvation protein
Synonym(s): Dps, PexB, Vtm, stationary phase nucleoid protein that sequesters iron and protects DNA from damage
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol,bacterial nucleoid
Molecular weight: 18.695
Isoelectric point: 6.008
Motif(s):
 
Type Positions Sequence
18 -> 18 R
31 -> 166 ELLNRQVIQFIDLSLITKQAHWNMRGANFIAVHEMLDGFRTALIDHLDTMAERAVQLGGVALGTTQVINSKTPLKSYPLDIHNVQDHLKELADRYAIVANDVRKAIGEAKDDDTADILTAASRDLDKFLWFIESNI
2 -> 167 STAKLVKSKATNLLYTRNDVSDSEKKATVELLNRQVIQFIDLSLITKQAHWNMRGANFIAVHEMLDGFRTALIDHLDTMAERAVQLGGVALGTTQVINSKTPLKSYPLDIHNVQDHLKELADRYAIVANDVRKAIGEAKDDDTADILTAASRDLDKFLWFIESNIE
68 -> 68 G

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.7 - central intermediary metabolism --> 1.7.19 - incorporation of metal ions
  2 - information transfer --> 2.3 - protein related --> 2.3.7 - nucleoproteins, basic proteins
  5 - cell processes --> 5.5 - adaptations --> 5.5.3 - starvation
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0009295 - nucleoid
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0046872 - metal ion binding
GO:0016491 - oxidoreductase activity
GO:0008199 - ferric iron binding
GO:0016722 - oxidoreductase activity, oxidizing metal ions
GO:0042802 - identical protein binding
biological_process GO:0006950 - response to stress
GO:0042594 - response to starvation
GO:0006879 - cellular iron ion homeostasis
GO:0030261 - chromosome condensation
GO:0055114 - oxidation-reduction process
Note(s): Note(s): ...[more].
External database links:  
DIP:
 DIP-35919N
ECOCYC:
 EG11415-MONOMER
ECOLIWIKI:
 b0812
INTERPRO:
 IPR012347
INTERPRO:
 IPR023188
INTERPRO:
 IPR002177
INTERPRO:
 IPR009078
INTERPRO:
 IPR023067
INTERPRO:
 IPR008331
MINT:
 P0ABT2
MODBASE:
 P0ABT2
PANTHER:
 PTHR42932
PDB:
 5XGO
PDB:
 1L8I
PDB:
 2W9R
PDB:
 1L8H
PDB:
 3O2H
PDB:
 1DPS
PDB:
 1F30
PDB:
 1F33
PDB:
 1JRE
PDB:
 1JTS
PFAM:
 PF00210
PRIDE:
 P0ABT2
PRINTS:
 PR01346
PRODB:
 PRO_000022478
PROSITE:
 PS00819
PROSITE:
 PS00818
REFSEQ:
 NP_415333
SMR:
 P0ABT2
UNIPROT:
 P0ABT2


Operon      
Name: dps         
Operon arrangement:
Transcription unit        Promoter
dps
dps


Transcriptional Regulation      
Display Regulation             
Activated by: IHF, OxyR
Repressed by: H-NS, MntR, Fis
Growth Conditions:

[1] 

C: Escherichia coli| M9 minimal medium| glucose 0.4%| 37.0 C| exponential phase
E: Escherichia coli| M9 minimal medium| hydrogen peroxide 120 µM; glucose 0.4%| 37.0 C| exponential phase

[2] 

C: Escherichia coli| multicopy plasmid pAMC35 (pexB) mutant| minimal medium| glucose| 37.0 C| stationary phase
E: Escherichia coli| rpoS knockout mutant; multicopy plasmid pAMC35 (pexB) mutant| minimal medium| glucose| 37.0 C| stationary phase

[3] 

C: Escherichia coli| MOPS| glucose| 37.0 C
E: Escherichia coli| MOPS| 37.0 C

[4] 

C: Escherichia coli| M9 minimal medium| glucose 0.4%| 37.0 C| exponential phase
E: Escherichia coli| M9 minimal medium| glucose 0.4%; sodium chloride 0.35 M| 37.0 C| exponential phase

[5] 

C: Escherichia coli| MOPS| 37.0 C
E: Escherichia coli| MOPS| glucose 0.05%| 37.0 C

[6] 

C: Escherichia coli| rpoS knockout mutant| M9 minimal medium| glucose 0.4%| 37.0 C| exponential phase
E: Escherichia coli| rpoS knockout mutant| M9 minimal medium| hydrogen peroxide 120 µM; glucose 0.4%| 37.0 C| exponential phase

[7] 

C: Escherichia coli| LB medium| glucose| 37.0 C
E: Escherichia coli| LB medium| 37.0 C

[8] 

C: Escherichia coli| MOPS| 37.0 C
E: Escherichia coli| MOPS| acetate 0.009%| 37.0 C

[9] 

C: Escherichia coli| M9 minimal medium| glucose 0.4%; sodium chloride 0.35 M| 37.0 C| exponential phase
E: Escherichia coli| rpoS knockout mutant| M9 minimal medium| glucose 0.4%; sodium chloride 0.35 M| 37.0 C| exponential phase

[10] 

C: Escherichia coli| multicopy plasmid pAMC35 (pexB) mutant| LB medium| 37.0 C| stationary phase
E: Escherichia coli| rpoS knockout mutant; multicopy plasmid pAMC35 (pexB) mutant| LB medium| 37.0 C| stationary phase


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_971 848936 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_972 (cluster) 848945 reverse For this promoter, there
Read more > 		[RS-EPT-CBR] [2]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Grainger DC., Goldberg MD., Lee DJ., Busby SJ., 2008, Selective repression by Fis and H-NS at the Escherichia coli dps promoter., Mol Microbiol 68(6):1366-77

 [2] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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