RegulonDB RegulonDB 11.1: Gene Form
   

trmD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

trmD rimM rplS TSS_2951 TSS_2951 TSS_2950 TSS_2950 TSS_2949 TSS_2949 TSS_2948 TSS_2948 rplSp1 rplSp1 TSS_2947 TSS_2947

Gene      
Name: trmD    Texpresso search in the literature
Synonym(s): ECK2604, EG11023, b2607
Genome position(nucleotides): 2744572 <-- 2745339
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.39
External database links:  
ASAP:
 ABE-0008576
CGSC:
 76
ECHOBASE:
 EB1016
ECOLIHUB:
 trmD
OU-MICROARRAY:
 b2607
STRING:
 511145.b2607
COLOMBOS: trmD


Product      
Name: tRNA m1G37 methyltransferase
Synonym(s): TrmD
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 28.422
Isoelectric point: 5.588
Motif(s):
 
Type Positions Sequence Comment
23 -> 221 GRAVKNGLLSIQSWSPRDFTHDRHRTVDDRPYGGGPGMLMMVQPLRDAIHAAKAAAGEGAKVIYLSPQGRKLDQAGVSELATNQKLILVCGRYEGIDERVIQTEIDEEWSIGDYVLSGGELPAMTLIDSVSRFIPGVLGHEASATEDSFAEGLLDCPHYTRPEVLEGMEVPPVLLSGNHAEIRRWRLKQSLGRTWLRRP
59 -> 59 G UniProt: Loss of activity..
91 -> 91 G UniProt: Loss of activity; no effect on tRNA binding..
114 -> 114 R UniProt: Loss of activity..
115 -> 115 Y UniProt: Increases Km for S-adenosyl-L-methionine 24-fold..

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.3 - RNA modification
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0008168 - methyltransferase activity
GO:0016740 - transferase activity
GO:0009019 - tRNA (guanine-N1-)-methyltransferase activity
GO:0000287 - magnesium ion binding
GO:0042802 - identical protein binding
GO:0042803 - protein homodimerization activity
GO:0052906 - tRNA (guanine(37)-N(1))-methyltransferase activity
biological_process GO:0006400 - tRNA modification
GO:0030488 - tRNA methylation
GO:0008033 - tRNA processing
GO:0032259 - methylation
GO:0002939 - tRNA N1-guanine methylation
Note(s): Note(s): ...[more].
Reference(s): [1] Ashtawy HM., et al., 2018
[2] Christian T., et al., 2004
[3] Gamper HB., et al., 2015
[4] Hou YM. 2016
[5] Wang H., et al., 2020
External database links:  
ALPHAFOLD:
 P0A873
DIP:
 DIP-48264N
ECOCYC:
 EG11023-MONOMER
ECOLIWIKI:
 b2607
INTERPRO:
 IPR023148
INTERPRO:
 IPR002649
INTERPRO:
 IPR016009
INTERPRO:
 IPR029028
INTERPRO:
 IPR029026
MODBASE:
 P0A873
PANTHER:
 PTHR46417
PDB:
 1P9P
PFAM:
 PF01746
PRIDE:
 P0A873
REFSEQ:
 NP_417098
SMR:
 P0A873
UNIPROT:
 P0A873


Operon      
Name: rpsP-rimM-trmD-rplS         
Operon arrangement:
Transcription unit        Promoter
rpsP-rimM-trmD-rplS


Transcriptional Regulation      
Display Regulation             
Repressed by: FNR


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_2947 2744532 reverse nd [RS-EPT-CBR] [6]
  promoter rplSp1 2744642 reverse nd [COMP-AINF] [7]
  promoter TSS_2948 2744644 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_2949 2744647 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_2950 2744657 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_2951 2744665 reverse nd [RS-EPT-CBR] [6]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Ashtawy HM., Mahapatra NR., 2018, Boosted neural networks scoring functions for accurate ligand docking and ranking., J Bioinform Comput Biol 16(2):1850004

 [2] Christian T., Evilia C., Williams S., Hou YM., 2004, Distinct origins of tRNA(m1G37) methyltransferase., J Mol Biol 339(4):707-19

 [3] Gamper HB., Masuda I., Frenkel-Morgenstern M., Hou YM., 2015, The UGG Isoacceptor of tRNAPro Is Naturally Prone to Frameshifts., Int J Mol Sci 16(7):14866-83

 [4] Hou YM., 2016, Single-Turnover Kinetics of Methyl Transfer to tRNA by Methyltransferases., Methods Mol Biol 1421:79-96

 [5] Wang H., Li H., 2020, Mechanically tightening, untying and retying a protein trefoil knot by single-molecule force spectroscopy., Chem Sci 11(46):12512-12521

 [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.

 [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

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