RegulonDB RegulonDB 10.7: 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
OU-MICROARRAY:
b0812
PORTECO:
dps
REGULONDB:
b0812
STRING:
511145.b0812
M3D: dps
COLOMBOS: dps
PortEco: b0812


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: bacterial nucleoid,cytosol
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:0005623 - cell
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:
IPR008331
INTERPRO:
IPR023188
INTERPRO:
IPR009078
INTERPRO:
IPR012347
INTERPRO:
IPR023067
INTERPRO:
IPR002177
MINT:
P0ABT2
MODBASE:
P0ABT2
PANTHER:
PTHR42932
PDB:
5XGO
PDB:
3O2H
PDB:
2W9R
PDB:
1L8I
PDB:
1L8H
PDB:
1JTS
PDB:
1JRE
PDB:
1F33
PDB:
1F30
PDB:
1DPS
PFAM:
PF00210
PRIDE:
P0ABT2
PRINTS:
PR01346
PRODB:
PRO_000022478
PROSITE:
PS00818
PROSITE:
PS00819
PROTEINMODELPORTAL:
P0ABT2
REFSEQ:
NP_415333
SMR:
P0ABT2
UNIPROT:
P0ABT2


Operon      
Name: dps         
Operon arrangement:
Transcription unit        Promoter
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



Regulation by small RNA    
  Display Regulation
small RNA oxyS


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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