RegulonDB RegulonDB 11.2: Gene Form
   

ybeY gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

miaB ybeZ ybeX ybeY anti-anti-terminator anti-terminator terminator ybeZp ybeZp TSS_784 TSS_784 TSS_783 TSS_783 TSS_782 TSS_782 lntp4 lntp4

Gene      
Name: ybeY    Texpresso search in the literature
Synonym(s): ECK0651, G6362, b0659
Genome position(nucleotides): 691874 <-- 692341
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.71
External database links:  
ASAP:
 ABE-0002255
ECHOBASE:
 EB3419
ECOLIHUB:
 ybeY
OU-MICROARRAY:
 b0659
STRING:
 511145.b0659
COLOMBOS: ybeY


Product      
Name: endoribonuclease YbeY
Synonym(s): YbeY, endoribonuclease involved in maturation of 16S rRNA and ribosome quality control
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 17.526
Isoelectric point: 3.948
Motif(s):
 
Type Positions Sequence Comment
20 -> 142 EESQFQTWLNAVIPQFQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIML
59 -> 59 R UniProt: Loss of activity..
114 -> 114 H UniProt: Loss of activity..
118 -> 118 H UniProt: No change in activity..
124 -> 124 H UniProt: No change in activity..

 
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:0004518 - nuclease activity
GO:0004519 - endonuclease activity
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0046872 - metal ion binding
GO:0016151 - nickel cation binding
GO:0008270 - zinc ion binding
GO:0004521 - endoribonuclease activity
GO:0004222 - metalloendopeptidase activity
GO:0016892 - endoribonuclease activity, producing 3'-phosphomonoesters
biological_process GO:0006412 - translation
GO:0006508 - proteolysis
GO:0009408 - response to heat
GO:0031564 - transcription antitermination
GO:0042254 - ribosome biogenesis
GO:0006364 - rRNA processing
GO:0042274 - ribosomal small subunit biogenesis
GO:0030490 - maturation of SSU-rRNA
GO:0000478 - endonucleolytic cleavage involved in rRNA processing
Note(s): Note(s): ...[more].
Evidence: [EXP-IDA] Inferred from direct assay
[EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Bobrovskyy M., et al., 2015
[2] Grinwald M., et al., 2013
[3] Jacob AI., et al., 2013
[4] Prossliner T., et al., 2021
[5] Rasouly A., et al., 2009
[6] Vercruysse M., et al., 2016
External database links:  
ALPHAFOLD:
 P0A898
DIP:
 DIP-48144N
ECOCYC:
 G6362-MONOMER
ECOLIWIKI:
 b0659
INTERPRO:
 IPR002036
INTERPRO:
 IPR023091
INTERPRO:
 IPR020549
MODBASE:
 P0A898
PANTHER:
 PTHR46986
PDB:
 1XM5
PFAM:
 PF02130
PRIDE:
 P0A898
PROSITE:
 PS01306
REFSEQ:
 NP_415192
SMR:
 P0A898
UNIPROT:
 P0A898


Operon      
Name: ybeZYX-lnt         
Operon arrangement:
Transcription unit        Promoter
ybeZYX-lnt
ybeX-lnt
ybeZY


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 lntp4 690984 reverse nd [COMP-AINF] [7]
  promoter TSS_782 691877 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_783 693429 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_784 693431 reverse nd [RS-EPT-CBR] [8]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] Bobrovskyy M., Vanderpool CK., Richards GR., 2015, Small RNAs Regulate Primary and Secondary Metabolism in Gram-negative Bacteria., Microbiol Spectr 3(3)

 [2] Grinwald M., Ron EZ., 2013, The Escherichia coli Translation-Associated Heat Shock Protein YbeY Is Involved in rRNA Transcription Antitermination., PLoS One 8(4):e62297

 [3] Jacob AI., Kohrer C., Davies BW., Rajbhandary UL., Walker GC., 2013, Conserved Bacterial RNase YbeY Plays Key Roles in 70S Ribosome Quality Control and 16S rRNA Maturation., Mol Cell 49(3):427-38

 [4] Prossliner T., Gerdes K., Sorensen MA., Winther KS., 2021, Hibernation factors directly block ribonucleases from entering the ribosome in response to starvation., Nucleic Acids Res 49(4):2226-2239

 [5] Rasouly A., Schonbrun M., Shenhar Y., Ron EZ., 2009, YbeY, a heat shock protein involved in translation in Escherichia coli., J Bacteriol 191(8):2649-55

 [6] Vercruysse M., Kohrer C., Shen Y., Proulx S., Ghosal A., Davies BW., RajBhandary UL., Walker GC., 2016, Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in Escherichia coli., MBio 7(6)

 [7] 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

 [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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