RegulonDB RegulonDB 10.10: Gene Form
   

yqgF gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yggR gshB yqgE yqgF terminator anti-terminator TSS_3277 (cluster) TSS_3277 (cluster) TSS_3276 (cluster) TSS_3276 (cluster) yqgEp3 yqgEp3 TSS_3275 (cluster) TSS_3275 (cluster) TSS_3274 TSS_3274 TSS_3273 TSS_3273

Gene      
Name: yqgF    Texpresso search in the literature
Synonym(s): ECK2944, G7525, b2949
Genome position(nucleotides): 3093500 --> 3093916 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.0
External database links:  
ASAP:
ABE-0009672
ECHOBASE:
EB3075
ECOLIHUB:
yqgF
OU-MICROARRAY:
b2949
STRING:
511145.b2949
COLOMBOS: yqgF


Product      
Name: ribonuclease H-like domain-containing nuclease
Synonym(s): DNA damage response protein YqgF, YqgF, putative pre-16S rRNA nuclease
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 15.186
Isoelectric point: 7.688
Motif(s):
 
Type Positions Sequence
9 -> 9 D
41 -> 41 D
103 -> 103 A
105 -> 105 S
96 -> 96 E

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.6 - rRNA, stable RNA
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0004518 - nuclease activity
GO:0016788 - hydrolase activity, acting on ester bonds
GO:0005515 - protein binding
GO:0016787 - hydrolase activity
GO:0008296 - 3'-5'-exodeoxyribonuclease activity
biological_process GO:0006139 - nucleobase-containing compound metabolic process
GO:0006259 - DNA metabolic process
GO:0006974 - cellular response to DNA damage stimulus
GO:0031564 - transcription antitermination
GO:0042254 - ribosome biogenesis
GO:0006364 - rRNA processing
GO:0090305 - nucleic acid phosphodiester bond hydrolysis
GO:0000967 - rRNA 5'-end processing
Note(s): Note(s): ...[more].
Evidence: [IDA] Inferred from direct assay
[IGI] Inferred from genetic interaction
Reference(s): [1] Gil R., et al., 2004
[2] Iwamoto A., et al., 2012
[3] Kurata T., et al., 2018
[4] Kurata T., et al., 2015
[5] McClung DJ., et al., 2016
[6] Nautiyal A., et al., 2016
External database links:  
ECOCYC:
G7525-MONOMER
ECOLIWIKI:
b2949
INTERPRO:
IPR012337
INTERPRO:
IPR037027
INTERPRO:
IPR006641
INTERPRO:
IPR005227
MODBASE:
P0A8I1
PANTHER:
PTHR33317
PDB:
1NU0
PDB:
1NMN
PDB:
1OVQ
PFAM:
PF03652
PRIDE:
P0A8I1
REFSEQ:
NP_417424
SMART:
SM00732
SMR:
P0A8I1
UNIPROT:
P0A8I1


Operon      
Name: yqgEF         
Operon arrangement:
Transcription unit        Promoter
yqgEF


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_3273 3092076 forward nd [RS-EPT-CBR] [7]
  promoter TSS_3274 3092824 forward nd [RS-EPT-CBR] [7]
  promoter TSS_3275 (cluster) 3092826 forward nd [RS-EPT-CBR] [7]
  promoter yqgEp3 3092884 forward nd [ICWHO] [8]
  promoter TSS_3276 (cluster) 3092900 forward nd [RS-EPT-CBR] [7]
  promoter TSS_3277 (cluster) 3092907 forward nd [RS-EPT-CBR] [7]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Gil R., Silva FJ., Pereto J., Moya A., 2004, Determination of the core of a minimal bacterial gene set., Microbiol Mol Biol Rev 68(3):518-37, table of contents

 [2] Iwamoto A., Osawa A., Kawai M., Honda H., Yoshida S., Furuya N., Kato J., 2012, Mutations in the essential Escherichia coli gene, yqgF, and their effects on transcription., J Mol Microbiol Biotechnol 22(1):17-23

 [3] Kurata T., Nakanishi S., Hashimoto M., Taoka M., Isobe T., Kato JI., 2018, Subunit Composition of Ribosome in the yqgF Mutant Is Deficient in pre-16S rRNA Processing of Escherichia coli., J Mol Microbiol Biotechnol 28(4):179-182

 [4] Kurata T., Nakanishi S., Hashimoto M., Taoka M., Yamazaki Y., Isobe T., Kato J., 2015, Novel essential gene Involved in 16S rRNA processing in Escherichia coli., J Mol Biol 427(4):955-65

 [5] McClung DJ., Calixto A., Mosera MN., Kumar R., Neidle EL., Elliott KT., 2016, Novel heterologous bacterial system reveals enhanced susceptibility to DNA damage mediated by yqgF, a nearly ubiquitous and often essential gene., Microbiology 162(10):1808-1821

 [6] Nautiyal A., Rani PS., Sharples GJ., Muniyappa K., 2016, Mycobacterium tuberculosis RuvX is a Holliday junction resolvase formed by dimerisation of the monomeric YqgF nuclease domain., Mol Microbiol 100(4):656-74

 [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.

 [8] 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


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