RegulonDB RegulonDB 10.10: Gene Form
   

rbfA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

infB truB rbfA rpsO ppGpp Cis-reg; leader anti-anti-terminator anti-terminator terminator anti-anti-terminator anti-terminator TSS_3465 TSS_3465 TSS_3464 (cluster) TSS_3464 (cluster) TSS_3463 TSS_3463 TSS_3462 TSS_3462 TSS_3461 TSS_3461 TSS_3460 TSS_3460 TSS_3459 TSS_3459 TSS_3458 TSS_3458 TSS_3457 TSS_3457 TSS_3456 TSS_3456 TSS_3455 TSS_3455 TSS_3454 TSS_3454 TSS_3453 TSS_3453 rpsOp rpsOp

Gene      
Name: rbfA    Texpresso search in the literature
Synonym(s): ECK3156, EG11178, b3167, sdr-43, yhbB
Genome position(nucleotides): 3312777 <-- 3313178 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.99
External database links:  
ASAP:
 ABE-0010406
CGSC:
 36919
ECHOBASE:
 EB1165
ECOLIHUB:
 rbfA
OU-MICROARRAY:
 b3167
STRING:
 511145.b3167
COLOMBOS: rbfA


Product      
Name: 30S ribosome binding factor
Synonym(s): RbfA, YhbB
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 15.154
Isoelectric point: 5.982
Motif(s):
 
Type Positions Sequence
2 -> 133 AKEFGRPQRVAQEMQKEIALILQREIKDPRLGMMTTVSGVEMSRDLAYAKVYVTFLNDKDEDAVKAGIKALQEASGFIRSLLGKAMRLRIVPELTFFYDNSLVEGMRMSNLVTSVVKHDEERRVNPDDSKED
100 -> 100 D
109 -> 133 MSNLVTSVVKHDEERRVNPDDSKED
84 -> 84 G
7 -> 112 RPQRVAQEMQKEIALILQREIKDPRLGMMTTVSGVEMSRDLAYAKVYVTFLNDKDEDAVKAGIKALQEASGFIRSLLGKAMRLRIVPELTFFYDNSLVEGMRMSNL

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.6 - rRNA, stable RNA
  5 - cell processes --> 5.5 - adaptations --> 5.5.2 - temperature extremes
  6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0043024 - ribosomal small subunit binding
biological_process GO:0006974 - cellular response to DNA damage stimulus
GO:0042254 - ribosome biogenesis
GO:0009409 - response to cold
GO:0006364 - rRNA processing
GO:0042274 - ribosomal small subunit biogenesis
GO:0030490 - maturation of SSU-rRNA
Note(s): Note(s): ...[more].
Evidence: [IGI] Inferred from genetic interaction
[IMP] Inferred from mutant phenotype
Reference(s): [1] Bylund GO., et al., 1998
[2] Jain C. 2018
[3] Jeganathan A., et al., 2015
[4] Leong V., et al., 2013
[5] Razi A., et al., 2017
[6] Sharma IM., et al., 2020
[7] Thurlow B., et al., 2016
External database links:  
ECOCYC:
 EG11178-MONOMER
ECOLIWIKI:
 b3167
INTERPRO:
 IPR023799
INTERPRO:
 IPR000238
INTERPRO:
 IPR015946
INTERPRO:
 IPR020053
PANTHER:
 PTHR33515
PDB:
 1KKG
PFAM:
 PF02033
PRIDE:
 P0A7G2
PRODB:
 PRO_000023681
PROSITE:
 PS01319
REFSEQ:
 NP_417636
SMR:
 P0A7G2
UNIPROT:
 P0A7G2


Operon      
Name: metY-rimP-nusA-infB-rbfA-truB-rpsO-pnp         
Operon arrangement:
Transcription unit        Promoter
pnp
rpsO
rpsO-pnp
infB
nusA-infB
rimP-nusA-infB
metY
metY-yhbC-nusA-infB
metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp
metY
metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp


Transcriptional Regulation      
Display Regulation             
Activated by: Fis
Repressed by: CRP, ArgR


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_3453 3312149 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3454 3312155 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3455 3314593 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3456 3315518 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3457 3315522 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3458 3315577 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3459 3315601 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3460 3315649 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3461 3315652 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3462 3315673 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3463 3315804 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3464 (cluster) 3315809 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_3465 3315884 reverse 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] Bylund GO., Wipemo LC., Lundberg LA., Wikstrom PM., 1998, RimM and RbfA are essential for efficient processing of 16S rRNA in Escherichia coli., J Bacteriol 180(1):73-82

 [2] Jain C., 2018, Role of ribosome assembly in Escherichia coli ribosomal RNA degradation., Nucleic Acids Res 46(20):11048-11060

 [3] Jeganathan A., Razi A., Thurlow B., Ortega J., 2015, The C-terminal helix in the YjeQ zinc-finger domain catalyzes the release of RbfA during 30S ribosome subunit assembly., RNA 21(6):1203-16

 [4] Leong V., Kent M., Jomaa A., Ortega J., 2013, Escherichia coli rimM and yjeQ null strains accumulate immature 30S subunits of similar structure and protein complement., RNA 19(6):789-802

 [5] Razi A., Guarne A., Ortega J., 2017, The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly., Proc Natl Acad Sci U S A 114(17):E3396-E3403

 [6] Sharma IM., Woodson SA., 2020, RbfA and IF3 couple ribosome biogenesis and translation initiation to increase stress tolerance., Nucleic Acids Res 48(1):359-372

 [7] Thurlow B., Davis JH., Leong V., Moraes TF., Williamson JR., Ortega J., 2016, Binding properties of YjeQ (RsgA), RbfA, RimM and Era to assembly intermediates of the 30S subunit., Nucleic Acids Res 44(20):9918-9932

 [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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