RegulonDB RegulonDB 10.9: Gene Form
   

trmA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

Gene      
Name: trmA    Texpresso search in the literature
Synonym(s): ECK3957, EG11022, b3965, rT, rumT
Genome position(nucleotides): 4162170 <-- 4163270 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.86
External database links:  
ASAP:
ABE-0012983
CGSC:
79
ECHOBASE:
EB1015
ECOLIHUB:
trmA
OU-MICROARRAY:
b3965
STRING:
511145.b3965
COLOMBOS: trmA


Product      
Name: tRNA m5U54 methyltransferase
Synonym(s): RumT, TrmA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 41.967
Isoelectric point: 5.97
Motif(s):
 
Type Positions Sequence
10 -> 365 QYEAQLAEKVVRLQSMMAPFSDLVPEVFRSPVSHYRMRAEFRIWHDGDDLYHIIFDQQTKSRIRVDSFPAASELINQLMTAMIAGVRNNPVLRHKLFQIDYLTTLSNQAVVSLLYHKKLDDEWRQEAEALRDALRAQNLNVHLIGRATKTKIELDQDYIDERLPVAGKEMIYRQVENSFTQPNAAMNIQMLEWALDVTKGSKGDLLELYCGNGNFSLALARNFDRVLATEIAKPSVAAAQYNIAANHIDNVQIIRMAAEEFTQAMNGVREFNRLQGIDLKSYQCETIFVDPPRSGLDSETEKMVQAYPRILYISCNPETLCKNLETLSQTHKVERLALFDQFPYTHHMECGVLLTA
358 -> 358 E

 

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:0008168 - methyltransferase activity
GO:0016740 - transferase activity
GO:0008173 - RNA methyltransferase activity
GO:0000049 - tRNA binding
GO:0019843 - rRNA binding
GO:0030697 - S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity
biological_process GO:0061818 - tRNA folding
GO:0030488 - tRNA methylation
GO:0006396 - RNA processing
GO:0008033 - tRNA processing
GO:0032259 - methylation
Note(s): Note(s): ...[more].
Reference(s): [1] Gu X., et al., 1991
[2] Gustafsson C., et al., 1992
[3] Lindstrom PH., et al., 1985
[4] Thanedar S., et al., 2001
[5] Yao LJ., et al., 1997
External database links:  
DIP:
DIP-11031N
ECOCYC:
EG11022-MONOMER
ECOLIWIKI:
b3965
INTERPRO:
IPR011869
INTERPRO:
IPR010280
INTERPRO:
IPR030391
INTERPRO:
IPR029063
INTERPRO:
IPR030390
MODBASE:
P23003
PANTHER:
PTHR47790
PDB:
3BT7
PFAM:
PF05958
PRIDE:
P23003
PROSITE:
PS51687
PROSITE:
PS01231
PROSITE:
PS01230
REFSEQ:
NP_418400
SMR:
P23003
UNIPROT:
P23003


Operon      
Name: trmA         
Operon arrangement:
Transcription unit        Promoter
trmA


Transcriptional Regulation      
Display Regulation             
Activated by: Fis


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_4693 4162891 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_4694 4162924 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_4695 4163652 forward nd [RS-EPT-CBR] [6]


Reference(s)    

 [1] Gu X., Santi DV., 1991, Affinity chromatography of Escherichia coli (m5U54)-methyltransferase on tRNA-agarose., Protein Expr Purif 2(1):66-8

 [2] Gustafsson C., Warne SR., 1992, Physical map of the oxyR-trmA region (minute 89.3) of the Escherichia coli chromosome., J Bacteriol 174(23):7878-9

 [3] Lindstrom PH., Stuber D., Bjork GR., 1985, Genetic organization and transcription from the gene (trmA) responsible for synthesis of tRNA (uracil-5)-methyltransferase by Escherichia coli., J Bacteriol 164(3):1117-23

 [4] Thanedar S., Dineshkumar TK., Varshney U., 2001, The mere lack of rT modification in initiator tRNA does not facilitate formylation-independent initiation in Escherichia coli., J Bacteriol 183(24):7397-402

 [5] Yao LJ., James TL., Kealey JT., Santi DV., Schmitz U., 1997, The dynamic NMR structure of the T psi C-loop: implications for the specificity of tRNA methylation., J Biomol NMR 9(3):229-44

 [6] 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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