RegulonDB RegulonDB 11.0: Gene Form
   

pgrR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

mppA ycjY pgrR PgrR mppAp4 mppAp4 mppAp9 mppAp9 mppAp13 mppAp13 mppAp5 mppAp5 TSS_1754 TSS_1754 ycjYp6 ycjYp6 TSS_1753 (cluster) TSS_1753 (cluster) ycjZp7 ycjZp7

Gene      
Name: pgrR    Texpresso search in the literature
Synonym(s): ECK1325, G6664, b1328, ycjZ
Genome position(nucleotides): 1391991 --> 1392890
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 46.56
External database links:  
ASAP:
 ABE-0004457
ECHOBASE:
 EB3682
ECOLIHUB:
 ycjZ
OU-MICROARRAY:
 b1328
STRING:
 511145.b1328
COLOMBOS: pgrR


Product      
Name: DNA-binding transcriptional repressor PgrR
Synonym(s): PgrR, YcjZ
Sequence: Get amino acid sequence Fasta Format
Regulator Family: LysR
Cellular location: cytosol
Molecular weight: 33.482
Isoelectric point: 9.458
Motif(s):
 
Type Positions Sequence Comment
4 -> 61 EEIADLMAFVVVAEERSFTRAAARLSMAQSALSQIVRRIEERLGLRLLTRTTRSVVPT UniProt: HTH lysR-type.
8 -> 65 DLMAFVVVAEERSFTRAAARLSMAQSALSQIVRRIEERLGLRLLTRTTRSVVPTEAGE
21 -> 40 FTRAAARLSMAQSALSQIVR UniProt: H-T-H motif.
90 -> 294 NRPSGTIRITTVEHAAKTILLPAMRTFLKSHPEIDIQLTIDYGLTDVVSERFDAGVRLGGEMDKDMIAIRIGPDIPMAIVGSPDYFSRRSVPTSVSQLIDHQAINLYLPTSGTANRWRLIRGGREVRVRMEGQLLLNTIDLIIDAAIDGHGLAYLPYDQVERAIKEKKLIRVLDKFTPDLPGYHLYYPHRRHAGSAFSLFIDRLK

 
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
Gene Ontology Terms (GO)  
cellular_component 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:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0045892 - negative regulation of transcription, DNA-templated
GO:0071978 - bacterial-type flagellum-dependent swarming motility
Note(s): Note(s): ...[more].
Evidence: [APPPINH] Assay of protein partially-purified from its native host
[HIFS] Human inference of function from sequence
Reference(s): [1] Perez-Rueda E., et al., 2000
[2] Perez-Rueda E., et al., 2004
[3] Shimada T., et al., 2013
External database links:  
ALPHAFOLD:
 P77333
DIP:
 DIP-11617N
ECOCYC:
 G6664-MONOMER
ECOLIWIKI:
 b1328
INTERPRO:
 IPR036390
INTERPRO:
 IPR005119
INTERPRO:
 IPR036388
INTERPRO:
 IPR000847
MODBASE:
 P77333
PFAM:
 PF03466
PFAM:
 PF00126
PRIDE:
 P77333
PRINTS:
 PR00039
PROSITE:
 PS50931
REFSEQ:
 NP_415844
SMR:
 P77333
UNIPROT:
 P77333


Operon      
Name: pgrR         
Operon arrangement:
Transcription unit        Promoter
pgrR


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 ycjZp7 1391872 forward nd [ICWHO] [4]
  promoter TSS_1753 (cluster) 1391946 forward nd [RS-EPT-CBR] [5]
  promoter TSS_1754 1392990 reverse nd [RS-EPT-CBR] [5]
  promoter mppAp5 1393054 forward nd [ICWHO] [4]
  promoter mppAp13 1393121 forward nd [ICWHO] [4]
  promoter mppAp9 1393139 forward nd [ICWHO] [4]
  promoter mppAp4 1393204 forward nd [ICWHO] [4]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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


Reference(s)    

 [1] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47

 [2] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [3] Shimada T., Yamazaki K., Ishihama A., 2013, Novel regulator PgrR for switch control of peptidoglycan recycling in Escherichia coli., Genes Cells 18(2):123-34

 [4] 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

 [5] 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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