RegulonDB RegulonDB 10.9: Gene Form
   

soxR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ghxP soxR soxS ryjA AcrR SoxR SoxS SoxR anti-terminator anti-anti-terminator anti-anti-terminator anti-terminator terminator anti-anti-terminator anti-terminator terminator yjcDp5 yjcDp5 ghxPp ghxPp yjcDp6 yjcDp6 yjcDp7 yjcDp7 ryjAp ryjAp soxRp soxRp soxSp soxSp

Gene      
Name: soxR    Texpresso search in the literature
Synonym(s): ECK4055, EG10957, b4063, marC
Genome position(nucleotides): 4277469 --> 4277933 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.04
External database links:  
ASAP:
ABE-0013316
CGSC:
27798
ECHOBASE:
EB0950
ECOLIHUB:
soxR
OU-MICROARRAY:
b4063
STRING:
511145.b4063
COLOMBOS: soxR


Shine dalgarno      
Sequence: aagttaacttGAGGTAaagcgatttATG


Product      
Name: DNA-binding transcriptional dual regulator SoxR
Synonym(s): MarC, SoxR
Sequence: Get amino acid sequence Fasta Format
Regulator Family: MerR
Cellular location: cytosol
Molecular weight: 17.15
Isoelectric point: 9.311
Motif(s):
 
Type Positions Sequence
119 -> 130 CIGCGCLSRSDC
20 -> 20 R
54 -> 119 LRYVAIIKIAQRIGIPLATIGEAFGVLPEGHTLSAKEWKQLSSQWREELDRRIHTLVALRDELDGC
11 -> 79 LLTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGV
13 -> 49 TPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRY

 

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 --> 3.3.1 - operon
  5 - cell processes --> 5.5 - adaptations --> 5.5.6 - other (mechanical, nutritional, oxidative stress)
  5 - cell processes --> 5.6 - protection --> 5.6.2 - detoxification
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
molecular_function GO:0003677 - DNA binding
GO:0046872 - metal ion binding
GO:0051536 - iron-sulfur cluster binding
GO:0051537 - 2 iron, 2 sulfur cluster binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0006979 - response to oxidative stress
Note(s): Note(s): ...[more].
Evidence: [APPHINH] Assay of protein purified to homogeneity from its native host
Reference(s): [1] Amabile-Cuevas CF., et al., 1991
[2] Fuentes AM., et al., 2001
[3] Hidalgo E., et al., 1995
[4] Nunoshiba T., et al., 1992
[5] Wu J., et al., 1991
External database links:  
DIP:
DIP-29848N
ECOCYC:
PD04132
ECOLIWIKI:
b4063
INTERPRO:
IPR010211
INTERPRO:
IPR015358
INTERPRO:
IPR009061
INTERPRO:
IPR000551
MODBASE:
P0ACS2
PANTHER:
PTHR30204:SF0
PDB:
2ZHH
PDB:
2ZHG
PFAM:
PF09278
PFAM:
PF00376
PRIDE:
P0ACS2
PRINTS:
PR00040
PRODB:
PRO_000023969
PROSITE:
PS00552
PROSITE:
PS50937
REFSEQ:
NP_418487
SMART:
SM00422
SMR:
P0ACS2
UNIPROT:
P0ACS2


Operon      
Name: soxR         
Operon arrangement:
Transcription unit        Promoter
soxR


Transcriptional Regulation      
Display Regulation             
Repressed by: SoxR, Fur, FNR, AcrR
Growth Conditions:

[1] 

C: Escherichia coli| LB broth| 37.0 C
E: Escherichia coli| soxR knockout mutant; soxS knockout mutant| LB broth| 37.0 C

[2] 

C: Escherichia coli| LB broth| 37.0 C
E: Escherichia coli| soxR knockout mutant; soxS knockout mutant; plasmid pSE380 mutant| LB broth| 37.0 C

[3] 

C: Escherichia coli| soxR knockout mutant; soxS knockout mutant; ?(soxR)| exponential phase
E: Escherichia coli| soxR knockout mutant; soxS knockout mutant; ?(truncated soxR)| exponential phase

[4] 

C: Escherichia coli| LB broth| paraquat 0.25 mM| 37.0 C
E: Escherichia coli| soxR knockout mutant; soxS knockout mutant; plasmid pSE380 mutant| LB broth| paraquat 0.25 mM| 37.0 C

[5] 

C: Escherichia coli| soxR knockout mutant; soxS knockout mutant; plasmid pSE380 mutant| LB broth| paraquat 0.25 mM| 37.0 C
E: Escherichia coli| soxR knockout mutant; soxS knockout mutant; plasmid pSXR (IPTG-induced soxR) mutant| LB broth| paraquat 0.25 mM| 37.0 C

[6] 

C: Escherichia coli| soxR knockout mutant; soxS knockout mutant; plasmid pSE380 mutant| LB broth| 37.0 C
E: Escherichia coli| soxR knockout mutant; soxS knockout mutant; plasmid pSXR (IPTG-induced soxR) mutant| LB broth| 37.0 C

[7] 

C: Escherichia coli| LB broth| paraquat 0.25 mM| 37.0 C
E: Escherichia coli| soxR knockout mutant; soxS knockout mutant| LB broth| paraquat 0.25 mM| 37.0 C



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 yjcDp7 4278314 forward Similarity to the consensus
Read more >
[ICWHO] [6]
  promoter yjcDp6 4278318 forward Similarity to the consensus
Read more >
[ICWHO] [6]
  promoter yjcDp5 4278466 forward Similarity to the consensus
Read more >
[ICWHO] [6]


Evidence    

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Amabile-Cuevas CF., Demple B., 1991, Molecular characterization of the soxRS genes of Escherichia coli: two genes control a superoxide stress regulon., Nucleic Acids Res 19(16):4479-84

 [2] Fuentes AM., Diaz-Mejia JJ., Maldonado-Rodriguez R., Amabile-Cuevas CF., 2001, Differential activities of the SoxR protein of Escherichia coli: SoxS is not required for gene activation under iron deprivation., FEMS Microbiol Lett 201(2):271-5

 [3] Hidalgo E., Bollinger JM., Bradley TM., Walsh CT., Demple B., 1995, Binuclear [2Fe-2S] clusters in the Escherichia coli SoxR protein and role of the metal centers in transcription., J Biol Chem 270(36):20908-14

 [4] Nunoshiba T., Hidalgo E., Amabile Cuevas CF., Demple B., 1992, Two-stage control of an oxidative stress regulon: the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS regulatory gene., J Bacteriol 174(19):6054-60

 [5] Wu J., Weiss B., 1991, Two divergently transcribed genes, soxR and soxS, control a superoxide response regulon of Escherichia coli., J Bacteriol 173(9):2864-71

 [6] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78


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