RegulonDB RegulonDB 11.1: Gene Form
   

prfA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

hemA prfA prmC ychQ TSS_1548 TSS_1548 TSS_1547 (cluster) TSS_1547 (cluster) ychQp ychQp TSS_1546 TSS_1546 TSS_1545 TSS_1545 TSS_1544 (cluster) TSS_1544 (cluster) TSS_1543 (cluster) TSS_1543 (cluster)

Gene      
Name: prfA    Texpresso search in the literature
Synonym(s): ECK1199, EG10761, b1211, sueB, uar, ups?
Genome position(nucleotides): 1265012 --> 1266094
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.0
External database links:  
ASAP:
 ABE-0004066
CGSC:
 14922
ECHOBASE:
 EB0754
ECOLIHUB:
 prfA
OU-MICROARRAY:
 b1211
STRING:
 511145.b1211
COLOMBOS: prfA


Product      
Name: peptide chain release factor RF1
Synonym(s): PrfA, SueB, Uar
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 40.517
Isoelectric point: 4.914
Motif(s):
 
Type Positions Sequence Comment
13 -> 203 HERHEEVQALLGDAQTIADQERFRALSREYAQLSDVSRCFTDWQQVQEDIETAQMMLDDPEMREMAQDELREAKEKSEQLEQQLQVLLLPKDPDDERNAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRWRVEIMSASEGEHGGYKEIIAKISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSACTV
72 -> 91 PEMREMAQDELREAKEKSEQ UniProt: In Ref. 7; M30785..
197 -> 197 H His197 is essential for ribosomal A site binding and peptide release |CITS: [20873815]|.
211 -> 211 D UniProt: In Ref. 3; AAC43437..
216 -> 321 DINPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLLGSGDRSDRNRTYNFPQGRVTDHR

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003747 - translation release factor activity
GO:0005515 - protein binding
GO:0043022 - ribosome binding
GO:0016149 - translation release factor activity, codon specific
biological_process GO:0006412 - translation
GO:0006415 - translational termination
Note(s): Note(s): ...[more].
Evidence: [EXP] Inferred from experiment
[EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
Reference(s): [1] Baggett NE., et al., 2017
[2] Florin T., et al., 2017
[3] Lajoie MJ., et al., 2013
[4] Mora L., et al., 2007
[5] Scolnick E., et al., 1968
[6] Shaw JJ., et al., 2007
[7] Wei Y., et al., 2016
External database links:  
ALPHAFOLD:
 P0A7I0
DIP:
 DIP-35936N
ECOCYC:
 EG10761-MONOMER
ECOLIWIKI:
 b1211
INTERPRO:
 IPR004373
INTERPRO:
 IPR005139
INTERPRO:
 IPR000352
MODBASE:
 P0A7I0
PDB:
 5O2R
PDB:
 6ORL
PDB:
 6GXN
PDB:
 6GXO
PDB:
 6GWT
PDB:
 6GXM
PDB:
 2B3T
PDB:
 5J30
PDB:
 5J3C
PDB:
 5J4D
PFAM:
 PF00472
PFAM:
 PF03462
PRIDE:
 P0A7I0
PRODB:
 PRO_000023588
PROSITE:
 PS00745
REFSEQ:
 NP_415729
SMART:
 SM00937
SMR:
 P0A7I0
SWISSMODEL:
 P0A7I0
UNIPROT:
 P0A7I0


Operon      
Name: hemA-prfA-prmC         
Operon arrangement:
Transcription unit        Promoter
hemA
hemA-prfA-prmC


Transcriptional Regulation      
Display Regulation             
Activated by: IHF, ArcA
Repressed by: FNR


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_1543 (cluster) 1264894 forward nd [RS-EPT-CBR] [8]
  promoter TSS_1544 (cluster) 1264899 forward nd [RS-EPT-CBR] [8]
  promoter TSS_1545 1265281 forward nd [RS-EPT-CBR] [8]
  promoter TSS_1546 1265487 forward nd [RS-EPT-CBR] [8]
  promoter TSS_1547 (cluster) 1267181 forward nd [RS-EPT-CBR] [8]
  promoter TSS_1548 1267190 forward nd [RS-EPT-CBR] [8]


Evidence    

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


Reference(s)    

 [1] Baggett NE., Zhang Y., Gross CA., 2017, Global analysis of translation termination in E. coli., PLoS Genet 13(3):e1006676

 [2] Florin T., Maracci C., Graf M., Karki P., Klepacki D., Berninghausen O., Beckmann R., Vazquez-Laslop N., Wilson DN., Rodnina MV., Mankin AS., 2017, An antimicrobial peptide that inhibits translation by trapping release factors on the ribosome., Nat Struct Mol Biol 24(9):752-757

 [3] Lajoie MJ., Rovner AJ., Goodman DB., Aerni HR., Haimovich AD., Kuznetsov G., Mercer JA., Wang HH., Carr PA., Mosberg JA., Rohland N., Schultz PG., Jacobson JM., Rinehart J., Church GM., Isaacs FJ., 2013, Genomically recoded organisms expand biological functions., Science 342(6156):357-60

 [4] Mora L., Heurgue-Hamard V., de Zamaroczy M., Kervestin S., Buckingham RH., 2007, Methylation of bacterial release factors RF1 and RF2 is required for normal translation termination in vivo., J Biol Chem 282(49):35638-45

 [5] Scolnick E., Tompkins R., Caskey T., Nirenberg M., 1968, Release factors differing in specificity for terminator codons., Proc Natl Acad Sci U S A 61(2):768-74

 [6] Shaw JJ., Green R., 2007, Two distinct components of release factor function uncovered by nucleophile partitioning analysis., Mol Cell 28(3):458-67

 [7] Wei Y., Wang J., Xia X., 2016, Coevolution between Stop Codon Usage and Release Factors in Bacterial Species., Mol Biol Evol 33(9):2357-67

 [8] 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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