RegulonDB RegulonDB 10.8: Gene Form
   

truB 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: truB    Texpresso search in the literature
Synonym(s): ECK3155, EG11177, b3166, yhbA
Genome position(nucleotides): 3311833 <-- 3312777 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.49
External database links:  
ASAP:
ABE-0010404
CGSC:
35528
ECHOBASE:
EB1164
OU-MICROARRAY:
b3166
PortEco:
truB
STRING:
511145.b3166
COLOMBOS: truB


Product      
Name: tRNA pseudouridine55 synthase
Synonym(s): TruB, YhbA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 35.087
Isoelectric point: 5.779
Motif(s):
 
Type Positions Sequence
174 -> 174 C
58 -> 58 C
48 -> 48 D
181 -> 247 RTIIDDLGEKLGCGAHVIYLRRLAVSKYPVERMVTLEHLRELVEQAEQQDIPAAELLDPLLMPMDSP
19 -> 19 K

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.3 - RNA modification
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0106029 - tRNA pseudouridine synthase activity
GO:0016853 - isomerase activity
GO:0003723 - RNA binding
GO:0009982 - pseudouridine synthase activity
GO:0000049 - tRNA binding
biological_process GO:0061818 - tRNA folding
GO:0006400 - tRNA modification
GO:0009451 - RNA modification
GO:0001522 - pseudouridine synthesis
GO:0031119 - tRNA pseudouridine synthesis
GO:0006396 - RNA processing
GO:0008033 - tRNA processing
GO:1990481 - mRNA pseudouridine synthesis
Note(s): Note(s): ...[more].
Reference(s): [1] Addepalli B., et al., 2011
[2] Frendewey DA., et al., 1982
[3] Gustafsson C., et al., 1996
[4] Koonin EV. 1996
[5] McDonald MK., et al., 2011
[6] Spedaliere CJ., et al., 2004
External database links:  
ECOCYC:
EG11177-MONOMER
ECOLIWIKI:
b3166
INTERPRO:
IPR036974
INTERPRO:
IPR032819
INTERPRO:
IPR020103
INTERPRO:
IPR015947
INTERPRO:
IPR015240
INTERPRO:
IPR014780
INTERPRO:
IPR002501
MODBASE:
P60340
PANTHER:
PTHR13767
PDB:
1ZL3
PDB:
1R3F
PDB:
1K8W
PFAM:
PF09157
PFAM:
PF01509
PFAM:
PF16198
PRIDE:
P60340
PRODB:
PRO_000024126
REFSEQ:
NP_417635
SMR:
P60340
UNIPROT:
P60340


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


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] [7]
  promoter TSS_3454 3312155 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_3455 3314593 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_3456 3315518 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_3457 3315522 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_3458 3315577 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_3459 3315601 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_3460 3315649 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_3461 3315652 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_3462 3315673 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_3463 3315804 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_3464 (cluster) 3315809 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [7]
  promoter TSS_3465 3315884 reverse 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] Addepalli B., Limbach PA., 2011, Mass spectrometry-based quantification of pseudouridine in RNA., J Am Soc Mass Spectrom 22(8):1363-72

 [2] Frendewey DA., Kladianos DM., Moore VG., Kaiser II., 1982, Loss of tRNA 5-methyluridine methyltransferase and pseudouridine synthetase activities in 5-fluorouracil and 1-(tetrahydro-2-furanyl)-5-fluorouracil (ftorafur)-treated Escherichia coli., Biochim Biophys Acta 697(1):31-40

 [3] Gustafsson C., Reid R., Greene PJ., Santi DV., 1996, Identification of new RNA modifying enzymes by iterative genome search using known modifying enzymes as probes., Nucleic Acids Res 24(19):3756-62

 [4] Koonin EV., 1996, Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases., Nucleic Acids Res 24(12):2411-5

 [5] McDonald MK., Miracco EJ., Chen J., Xie Y., Mueller EG., 2011, The handling of the mechanistic probe 5-fluorouridine by the pseudouridine synthase TruA and its consistency with the handling of the same probe by the pseudouridine synthases TruB and RluA., Biochemistry 50(3):426-36

 [6] Spedaliere CJ., Ginter JM., Johnston MV., Mueller EG., 2004, The pseudouridine synthases: revisiting a mechanism that seemed settled., J Am Chem Soc 126(40):12758-9

 [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.


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