RegulonDB RegulonDB 11.1: Gene Form
   

trpR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

slt yjjX trpR TrpR trpRp trpRp TSS_5179 TSS_5179

Gene      
Name: trpR    Texpresso search in the literature
Synonym(s): ECK4385, EG11029, b4393, rtrY
Genome position(nucleotides): 4632760 --> 4633086
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.13
External database links:  
ASAP:
 ABE-0014408
CGSC:
 68
ECHOBASE:
 EB1022
ECOLIHUB:
 trpR
OU-MICROARRAY:
 b4393
STRING:
 511145.b4393
COLOMBOS: trpR


Product      
Name: DNA-binding transcriptional repressor TrpR
Synonym(s): RtrY, TrpR
Sequence: Get amino acid sequence Fasta Format
Regulator Family: TrpR
Cellular location: cytosol
Molecular weight: 12.355
Isoelectric point: 5.207
Motif(s):
 
Type Positions Sequence Comment
2 -> 108 AQQSPYSAAMAEQRHQEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLLKSD UniProt: Trp operon repressor.
17 -> 102 QEWLRFVDLLKNAYQNDLHLPLLNLMLTPDEREALGTRVRIVEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEE
26 -> 26 L UniProt: In Ref. 4; AAA72134..
56 -> 56 R UniProt: In Ref. 4; AAA72134..
68 -> 91 QRELKNELGAGIATITRGSNSLKA

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.1 - amino acids --> 1.5.1.15 - tryptophan
  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:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0043565 - sequence-specific DNA binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0045892 - negative regulation of transcription, DNA-templated
Reference(s): [1] Arrowsmith C., et al., 1991
[2] Arrowsmith CH., et al., 1990
[3] Borden KL., et al., 1992
[4] Gunsalus RP., et al., 1980
[5] Lawson CL., et al., 1988
[6] Luisi BF., et al., 1990
[7] Singleton CK., et al., 1980
[8] Zhang H., et al., 1994
[9] Zhang RG., et al., 1987
External database links:  
ALPHAFOLD:
 P0A881
DIP:
 DIP-48204N
ECOCYC:
 PD00423
ECOLIWIKI:
 b4393
INTERPRO:
 IPR000831
INTERPRO:
 IPR038116
INTERPRO:
 IPR010921
INTERPRO:
 IPR013335
PANTHER:
 PTHR38025
PDB:
 2OZ9
PDB:
 3SSW
PDB:
 3SSX
PDB:
 3WRP
PDB:
 6EJW
PDB:
 6EKP
PDB:
 6ELB
PDB:
 6ELF
PDB:
 6ELG
PDB:
 6ENI
PDB:
 6ENN
PDB:
 6F7F
PDB:
 6F7G
PDB:
 6F9K
PDB:
 6FAL
PDB:
 6ST6
PDB:
 6ST7
PDB:
 1ZT9
PDB:
 1WRT
PDB:
 1WRS
PDB:
 1WRP
PDB:
 1TRR
PDB:
 1TRO
PDB:
 1RCS
PDB:
 1MI7
PDB:
 1CO0
PDB:
 1JHG
PFAM:
 PF01371
PRIDE:
 P0A881
PRODB:
 PRO_000024124
REFSEQ:
 NP_418810
SMR:
 P0A881
UNIPROT:
 P0A881


Operon      
Name: trpR         
Operon arrangement:
Transcription unit        Promoter
trpR


Transcriptional Regulation      
Display Regulation             
Repressed by: TrpR


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_5179 4632698 forward nd [RS-EPT-CBR] [10]


Evidence    

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


Reference(s)    

 [1] Arrowsmith C., Pachter R., Altman R., Jardetzky O., 1991, The solution structures of Escherichia coli trp repressor and trp aporepressor at an intermediate resolution., Eur J Biochem 202(1):53-66

 [2] Arrowsmith CH., Pachter R., Altman RB., Iyer SB., Jardetzky O., 1990, Sequence-specific 1H NMR assignments and secondary structure in solution of Escherichia coli trp repressor., Biochemistry 29(27):6332-41

 [3] Borden KL., Bauer CJ., Frenkiel TA., Beckmann P., Lane AN., 1992, Sequence-specific NMR assignments of the trp repressor from Escherichia coli using three-dimensional 15N/1H heteronuclear techniques., Eur J Biochem 204(1):137-46

 [4] Gunsalus RP., Yanofsky C., 1980, Nucleotide sequence and expression of Escherichia coli trpR, the structural gene for the trp aporepressor., Proc Natl Acad Sci U S A 77(12):7117-21

 [5] Lawson CL., Sigler PB., 1988, The structure of trp pseudorepressor at 1.65A shows why indole propionate acts as a trp 'inducer'., Nature 333(6176):869-71

 [6] Luisi BF., Sigler PB., 1990, The stereochemistry and biochemistry of the trp repressor-operator complex., Biochim Biophys Acta 1048(2-3):113-26

 [7] Singleton CK., Roeder WD., Bogosian G., Somerville RL., Weith HL., 1980, DNA sequence of the E. coli trpR gene and prediction of the amino acid sequence of Trp repressor., Nucleic Acids Res 8(7):1551-60

 [8] Zhang H., Zhao D., Revington M., Lee W., Jia X., Arrowsmith C., Jardetzky O., 1994, The solution structures of the trp repressor-operator DNA complex., J Mol Biol 238(4):592-614

 [9] Zhang RG., Joachimiak A., Lawson CL., Schevitz RW., Otwinowski Z., Sigler PB., 1987, The crystal structure of trp aporepressor at 1.8 A shows how binding tryptophan enhances DNA affinity., Nature 327(6123):591-7

 [10] 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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