RegulonDB RegulonDB 10.9: Gene Form
   

oxyR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

sthA oxyR fabR oxyS OxyR OxyR terminator terminator TSS_4692 TSS_4692 TSS_4691 TSS_4691 TSS_4690 TSS_4690 TSS_4689 TSS_4689 TSS_4688 TSS_4688 sthAp sthAp oxyRp oxyRp oxySp oxySp

Gene      
Name: oxyR    Texpresso search in the literature
Synonym(s): ECK3953, EG10681, b3961, momR, mor
Genome position(nucleotides): 4158490 --> 4159407 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
55.45
External database links:  
ASAP:
ABE-0012973
CGSC:
28841
ECHOBASE:
EB0675
ECOLIHUB:
oxyR
OU-MICROARRAY:
b3961
STRING:
511145.b3961
COLOMBOS: oxyR


Product      
Name: DNA-binding transcriptional dual regulator OxyR
Synonym(s): MomR, Mor, OxyR, bifunctional regulatory protein sensor for oxidative stress
Sequence: Get amino acid sequence Fasta Format
Regulator Family: LysR
Cellular location: cytosol
Molecular weight: 34.276
Isoelectric point: 6.376
Motif(s):
 
Type Positions Sequence
18 -> 37 FRRAADSCHVSQPTLSGQIR
249 -> 249 R
1 -> 58 MNIRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFT
3 -> 61 IRDLEYLVALAEHRHFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERTSRKVLFTQAG
199 -> 199 C

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.2 - regulon
  5 - cell processes --> 5.5 - adaptations --> 5.5.6 - other (mechanical, nutritional, oxidative stress)
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
GO:0032993 - protein-DNA complex
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0003700 - DNA-binding transcription factor activity
GO:0000986 - bacterial-type cis-regulatory region sequence-specific DNA binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0006974 - cellular response to DNA damage stimulus
GO:0006979 - response to oxidative stress
GO:0051409 - response to nitrosative stress
GO:2000142 - regulation of DNA-templated transcription, initiation
Note(s): Note(s): ...[more].
Evidence: [APPHINH] Assay of protein purified to homogeneity from its native host
Reference(s): [1] Blattner FR., et al., 1993
[2] Bolker M., et al., 1989
[3] Christman MF., et al., 1989
[4] Seth D., et al., 2012
[5] Tao K., et al., 1993
[6] Tao K., et al., 1991
[7] Tao K., et al., 1989
[8] Warne SR., et al., 1990
External database links:  
DIP:
DIP-10419N
ECOCYC:
PD00214
ECOLIWIKI:
b3961
INTERPRO:
IPR036388
INTERPRO:
IPR036390
INTERPRO:
IPR000847
INTERPRO:
IPR005119
MODBASE:
P0ACQ4
PDB:
1I6A
PDB:
1I69
PFAM:
PF03466
PFAM:
PF00126
PRIDE:
P0ACQ4
PRINTS:
PR00039
PRODB:
PRO_000023474
PROSITE:
PS50931
REFSEQ:
NP_418396
SMR:
P0ACQ4
UNIPROT:
P0ACQ4


Operon      
Name: oxyR         
Operon arrangement:
Transcription unit        Promoter
oxyR
oxyR


Transcriptional Regulation      
Display Regulation             
Activated by: CRP
Repressed by: OxyR
Growth Conditions:

[1] 

C: Escherichia coli| LB medium| mid exponential phase
E: Escherichia coli| LB medium| hydrogen peroxide 100 µM| mid exponential phase



RNA cis-regulatory element    
Attenuation: Translational


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_4688 4161094 forward nd [RS-EPT-CBR] [9]
  promoter TSS_4689 4161458 forward nd [RS-EPT-CBR] [9]
  promoter TSS_4690 4161554 forward nd [RS-EPT-CBR] [9]
  promoter TSS_4691 4161556 forward nd [RS-EPT-CBR] [9]
  promoter TSS_4692 4161745 forward nd [RS-EPT-CBR] [9]


Evidence    

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



Reference(s)    

 [1] Blattner FR., Burland V., Plunkett G., Sofia HJ., Daniels DL., 1993, Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes., Nucleic Acids Res 21(23):5408-17

 [2] Bolker M., Kahmann R., 1989, The Escherichia coli regulatory protein OxyR discriminates between methylated and unmethylated states of the phage Mu mom promoter., EMBO J 8(8):2403-10

 [3] Christman MF., Storz G., Ames BN., 1989, OxyR, a positive regulator of hydrogen peroxide-inducible genes in Escherichia coli and Salmonella typhimurium, is homologous to a family of bacterial regulatory proteins., Proc Natl Acad Sci U S A 86(10):3484-8

 [4] Seth D., Hausladen A., Wang YJ., Stamler JS., 2012, Endogenous protein S-Nitrosylation in E. coli: regulation by OxyR., Science 336(6080):470-3

 [5] Tao K., Fujita N., Ishihama A., 1993, Involvement of the RNA polymerase alpha subunit C-terminal region in co-operative interaction and transcriptional activation with OxyR protein., Mol Microbiol 7(6):859-64

 [6] Tao K., Makino K., Yonei S., Nakata A., Shinagawa H., 1991, Purification and characterization of the Escherichia coli OxyR protein, the positive regulator for a hydrogen peroxide-inducible regulon., J Biochem 109(2):262-6

 [7] Tao K., Makino K., Yonei S., Nakata A., Shinagawa H., 1989, Molecular cloning and nucleotide sequencing of oxyR, the positive regulatory gene of a regulon for an adaptive response to oxidative stress in Escherichia coli: homologies between OxyR protein and a family of bacterial activator proteins., Mol Gen Genet 218(3):371-6

 [8] Warne SR., Varley JM., Boulnois GJ., Norton MG., 1990, Identification and characterization of a gene that controls colony morphology and auto-aggregation in Escherichia coli K12., J Gen Microbiol 136(3):455-62

 [9] 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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