RegulonDB RegulonDB 11.0: Gene Form
   

ubiU gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ubiU ubiV ubiT yhbS CsgD CsgD terminator TSS_3428 TSS_3428 yhbUp5 yhbUp5 ubiTp1 ubiTp1 yhbUp1 yhbUp1 TSS_3427 TSS_3427 ubiTp2 ubiTp2 yhbUp7 yhbUp7 TSS_3425 (cluster) TSS_3425 (cluster) TSS_3424 TSS_3424 TSS_3423 TSS_3423 TSS_3422 TSS_3422 TSS_3421 TSS_3421

Gene      
Name: ubiU    Texpresso search in the literature
Synonym(s): ECK3146, G7652, b3158, yhbU
Genome position(nucleotides): 3301485 --> 3302480
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 56.83
External database links:  
ASAP:
 ABE-0010380
ECHOBASE:
 EB2642
ECOLIHUB:
 yhbU
OU-MICROARRAY:
 b3158
STRING:
 511145.b3158
COLOMBOS: ubiU


Product      
Name: ubiquinone biosynthesis protein UbiU
Synonym(s): UbiU, YhbU, putative peptidase (collagenase-like), putative peptidase YhbU
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 37.047
Isoelectric point: 7.132
Motif(s):
 
Type Positions Sequence Comment
76 -> 330 RWQRAVDMAAQLGADALILADLAMLEYAAERYPHIERHVSVQASATNEEAINFYHRHFDVARVVLPRVLSIHQVKQLARVTPVPLEVFAFGSLCIMSEGRCYLSSYLTGESPNTIGACSPARFVRWQQTPQGLESRLNEVLIDRYQDGENAGYPTLCKGRYLVDGERYHALEEPTSLNTLELLPELMAANIASVKIEGRQRSPAYVSQVAKVWRQAIDRCKADPQNFVPQSAWMETLGSMSEGTQTTLGAYHRKW
169 -> 169 C UniProt: Decreases iron-sulfur binding; when associated with A-176..
176 -> 176 C UniProt: Alters ubiquinone synthesis in anaerobic conditions. Decreases iron-sulfur binding; when associated with A-169..
193 -> 193 C UniProt: Decreases iron-sulfur binding; when associated with A-232..
232 -> 232 C UniProt: Decreases iron-sulfur binding; when associated with A-193..

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.3 - cofactors, small molecule carriers --> 1.5.3.11 - menaquinone, ubiquinone
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0005515 - protein binding
GO:0046872 - metal ion binding
GO:0051536 - iron-sulfur cluster binding
GO:0051539 - 4 iron, 4 sulfur cluster binding
biological_process GO:0006744 - ubiquinone biosynthetic process
GO:0032150 - ubiquinone biosynthetic process from chorismate
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Pelosi L., et al., 2019
External database links:  
ALPHAFOLD:
 P45527
DIP:
 DIP-12268N
ECOCYC:
 G7652-MONOMER
ECOLIWIKI:
 b3158
INTERPRO:
 IPR036206
INTERPRO:
 IPR001539
INTERPRO:
 IPR043692
MODBASE:
 P45527
PFAM:
 PF01136
PRIDE:
 P45527
PROSITE:
 PS01276
REFSEQ:
 NP_417627
SMR:
 P45527
UNIPROT:
 P45527


Operon      
Name: ubiUV         
Operon arrangement:
Transcription unit        Promoter
ubiUV


RNA cis-regulatory element    
Attenuation: Translational


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_3421 3300908 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3422 3300960 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3423 3300965 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3424 3300967 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_3425 (cluster) 3301010 reverse nd [RS-EPT-CBR] [2]
  promoter yhbUp7 3301279 forward nd [ICWHO] [3]
  promoter TSS_3427 3301317 reverse nd [RS-EPT-CBR] [2]
  promoter yhbUp1 3301329 forward nd [ICWHO] [3]
  promoter yhbUp5 3301437 forward nd [ICWHO] [3]
  promoter TSS_3428 3301439 forward nd [RS-EPT-CBR] [2]


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] Pelosi L., Vo CD., Abby SS., Loiseau L., Rascalou B., Hajj Chehade M., Faivre B., Gousse M., Chenal C., Touati N., Binet L., Cornu D., Fyfe CD., Fontecave M., Barras F., Lombard M., Pierrel F., 2019, Ubiquinone Biosynthesis over the Entire O2 Range: Characterization of a Conserved O2 -Independent Pathway., MBio 10(4)

 [2] 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.

 [3] 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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