RegulonDB RegulonDB 10.9: Gene Form
   

arfA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

trkA zntR mscL arfA anti-terminator terminator terminator anti-terminator anti-anti-terminator arfAp3 arfAp3 TSS_3610 TSS_3610 mscLp mscLp TSS_3609 TSS_3609 TSS_3608 TSS_3608

Gene      
Name: arfA    Texpresso search in the literature
Synonym(s): ECK3278, G0-10465, b4550, yhdL
Genome position(nucleotides): 3438431 <-- 3438649 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
43.38
External database links:  
ASAP:
ABE-0285071
ECHOBASE:
EB1911
ECOLIHUB:
yhdL
STRING:
511145.b4550
COLOMBOS: arfA


Product      
Name: alternative ribosome-rescue factor A
Synonym(s): ArfA, YhdL
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 8.171
Isoelectric point: 10.994
Motif(s):
 
Type Positions Sequence
30 -> 30 E
36 -> 36 K
39 -> 39 Y
4 -> 45 YQHTKGQIKDNAIEALLHDPLFRQRVEKNKKGKGSYMRKGKH
11 -> 11 I

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
Gene Ontology Terms (GO)  
molecular_function GO:0003723 - RNA binding
GO:0000049 - tRNA binding
GO:0019843 - rRNA binding
GO:0043023 - ribosomal large subunit binding
biological_process GO:0006417 - regulation of translation
GO:0072344 - rescue of stalled ribosome
Note(s): Note(s): ...[more].
Evidence: [IDA] Inferred from direct assay
Reference(s): [1] Abo T., et al., 2015
[2] Chadani Y., et al., 2010
[3] Kurita D., et al., 2020
[4] Li J., et al., 2017
[5] Ma NJ., et al., 2018
[6] Morra R., et al., 2018
External database links:  
ECOCYC:
MONOMER0-2687
ECOLIWIKI:
b4550
INTERPRO:
IPR005589
PDB:
5MGP
PDB:
5U4I
PDB:
5U4J
PDB:
5U9F
PDB:
5U9G
PDB:
6C4I
PDB:
5MDY
PDB:
5MDW
PDB:
5MDV
PDB:
5H5U
PFAM:
PF03889
PRIDE:
P36675
REFSEQ:
YP_588467
SMR:
P36675
UNIPROT:
P36675


Operon      
Name: arfA         
Operon arrangement:
Transcription unit        Promoter
arfA


RNA cis-regulatory element    
Attenuation: Transcriptional


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_3608 3437344 forward nd [RS-EPT-CBR] [7]
  promoter TSS_3609 3437352 forward nd [RS-EPT-CBR] [7]
  promoter TSS_3610 3438041 forward nd [RS-EPT-CBR] [7]


Evidence    

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



Reference(s)    

 [1] Abo T., Chadani Y., 2015, [Ribosome rescue systems in Escherichia coli]., Seikagaku 87(6):736-40

 [2] Chadani Y., Ono K., Ozawa S., Takahashi Y., Takai K., Nanamiya H., Tozawa Y., Kutsukake K., Abo T., 2010, Ribosome rescue by Escherichia coli ArfA (YhdL) in the absence of trans-translation system., Mol Microbiol 78(4):796-808

 [3] Kurita D., Abo T., Himeno H., 2020, Molecular determinants of Release Factor 2 for ArfA-mediated ribosome rescue., J Biol Chem

 [4] Li J., Zhang C., Huang P., Kuru E., Forster-Benson ETC., Li T., Church GM., 2017, Dissecting limiting factors of the Protein synthesis Using Recombinant Elements (PURE) system., Translation (Austin) 5(1):e1327006

 [5] Ma NJ., Hemez CF., Barber KW., Rinehart J., Isaacs FJ., 2018, Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue., Elife 7

 [6] Morra R., Del Carratore F., Muhamadali H., Horga LG., Halliwell S., Goodacre R., Breitling R., Dixon N., 2018, Translation Stress Positively Regulates MscL-Dependent Excretion of Cytoplasmic Proteins., mBio 9(1)

 [7] 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.


RegulonDB