RegulonDB RegulonDB 10.9: Gene Form
   

plaR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yiaK plaR ysaA CRP YiaJ IHF IHF CRP terminator yiaKp2 yiaKp2 yiaKp yiaKp yiaJp yiaJp TSS_4174 (cluster) TSS_4174 (cluster) TSS_4173 TSS_4173

Gene      
Name: plaR    Texpresso search in the literature
Synonym(s): ECK3563, EG12278, b3574, yiaJ
Genome position(nucleotides): 3741684 <-- 3742532 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.18
External database links:  
ASAP:
ABE-0011677
ECHOBASE:
EB2186
ECOLIHUB:
yiaJ
OU-MICROARRAY:
b3574
STRING:
511145.b3574
COLOMBOS: plaR


Shine dalgarno      
Sequence: gcgctaccatCAGGACgcgacaaAAT


Product      
Name: DNA-binding transcriptional repressor PlaR
Synonym(s): PlaR, YiaJ
Sequence: Get amino acid sequence Fasta Format
Regulator Family: IclR
Cellular location: cytosol
Molecular weight: 31.067
Isoelectric point: 6.912
Motif(s):
 
Type Positions Sequence
100 -> 272 IIHIAAPHLEALNIATGETINFSSREDDHAILIYKLEPTTGMLRTRAYIGQHMPLYCSAMGKIYMAFGHPDYVKSYWESHQHEIQPLTRNTITELPAMFDELAHIRESGAAMDREENELGVSCIAVPVFDIHGRVPYAVSISLSTSRLKQVGEKNLLKPLRETAQAISNELGF
143 -> 268 RTRAYIGQHMPLYCSAMGKIYMAFGHPDYVKSYWESHQHEIQPLTRNTITELPAMFDELAHIRESGAAMDREENELGVSCIAVPVFDIHGRVPYAVSISLSTSRLKQVGEKNLLKPLRETAQAISN
25 -> 74 SLFRGLMLIEILSNYPNGCPLAHLSELAGLNKSTVHRLLQGLQSCGYVTT
45 -> 64 LAHLSELAGLNKSTVHRLLQ
23 -> 85 SQSLFRGLMLIEILSNYPNGCPLAHLSELAGLNKSTVHRLLQGLQSCGYVTTAPAAGSYRLTT

 

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 --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0045892 - negative regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [APPH] Assay of protein purified to homogeneity
[GEA] Gene expression analysis
[IMP] Inferred from mutant phenotype
[IPI] Inferred from physical interaction
Reference(s): [1] Badia J., et al., 1998
[2] Gao Y., et al., 2018
[3] Ibanez E., et al., 2000
External database links:  
ECOCYC:
EG12278-MONOMER
ECOLIWIKI:
b3574
INTERPRO:
IPR029016
INTERPRO:
IPR036390
INTERPRO:
IPR036388
INTERPRO:
IPR014757
INTERPRO:
IPR005471
MODBASE:
P37671
PDB:
1YSQ
PFAM:
PF01614
PFAM:
PF09339
PRIDE:
P37671
PROSITE:
PS51078
PROSITE:
PS51077
REFSEQ:
NP_418031
SMART:
SM00346
SMR:
P37671
SWISSMODEL:
P37671
UNIPROT:
P37671


Operon      
Name: plaR         
Operon arrangement:
Transcription unit        Promoter
plaR


Transcriptional Regulation      
Display Regulation             
Repressed by: CRP, IHF, YiaJ
Growth Conditions:

[1] 

C:
E: Escherichia coli| chloroacetic acid| OD650 of 0.5

[2] 

C: Escherichia coli| yiaJ knockout mutant| chloroacetic acid| oxygen atom| OD600 of 0.5
E: Escherichia coli| yiaJ knockout mutant| chloroacetic acid| glucose 60 mM| oxygen atom| OD600 of 0.5

[3] 

C: Escherichia coli| chloroacetic acid| oxygen atom| OD600 of 0.5
E: Escherichia coli| chloroacetic acid| glucose 60 mM| oxygen atom| OD600 of 0.5

[4] 

C: Escherichia coli| chloroacetic acid| oxygen atom| OD600 of 0.5
E: Escherichia coli| yiaJ knockout mutant| chloroacetic acid| oxygen atom| OD600 of 0.5



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_4173 3741599 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_4174 (cluster) 3741605 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [4]


Evidence    

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



Reference(s)    

 [1] Badia J., Ibanez E., Sabate M., Baldoma L., Aguilar J., 1998, A rare 920-kilobase chromosomal inversion mediated by IS1 transposition causes constitutive expression of the yiaK-S operon for carbohydrate utilization in Escherichia coli., J Biol Chem 273(14):8376-81

 [2] Gao Y., Yurkovich JT., Seo SW., Kabimoldayev I., Drager A., Chen K., Sastry AV., Fang X., Mih N., Yang L., Eichner J., Cho BK., Kim D., Palsson BO., 2018, Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655., Nucleic Acids Res 46(20):10682-10696

 [3] Ibanez E., Campos E., Baldoma L., Aguilar J., Badia J., 2000, Regulation of expression of the yiaKLMNOPQRS operon for carbohydrate utilization in Escherichia coli: involvement of the main transcriptional factors., J Bacteriol 182(16):4617-24

 [4] 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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