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Literature summary extracted from

  • Hou, Y.; Masuda, I.; Gamper, H.
    Codon-specific translation by m1G37 methylation of tRNA (2019), Front. Genet., 10, 713 .
    View publication on PubMedView publication on EuropePMC

Protein Variants

EC Number Protein Variants Comment Organism
2.1.1.228 S88L mutant trmD harbors a mutation near the AdoMet binding site, the mutation prevents the enzyme from binding to the methyl donor and from performing the Mg2C-dependent methyl transfer. The reported observation supports a model of codon-specific translation in the 5'-leader ORF Salmonella enterica subsp. enterica serovar Typhimurium

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.1.1.228 Mg2+ required Escherichia coli
2.1.1.228 Mg2+ required, cells expressing the native trmD show more than a 6fold activation of transcription upon switching from high to low Mg2+ media, whereas cells expressing a S88L mutant trmD show less than a 2fold activation. For cells expressing the native trmD, the level of Mg2+ modulates the level of TrmD-dependent m1G37-tRNA synthesis, which in turn modulates the speed of ribosomal translation of m1G37-dependent codons in the 5'-leader ORF. At high Mg2+, TrmD is active and the abundantly synthesized m1G37-tRNA facilitates ribosomal translation through the 5'-leader ORF Salmonella enterica subsp. enterica serovar Typhimurium

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Escherichia coli
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Saccharomyces cerevisiae
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Salmonella enterica subsp. enterica serovar Typhimurium
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Saccharomyces cerevisiae ATCC 204508
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNAPro(UGG) Escherichia coli
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAPro(UGG)
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.1.1.228 Escherichia coli P0A873
-
-
2.1.1.228 Saccharomyces cerevisiae P38793
-
-
2.1.1.228 Saccharomyces cerevisiae ATCC 204508 P38793
-
-
2.1.1.228 Salmonella enterica subsp. enterica serovar Typhimurium P36245
-
-
2.1.1.228 Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720 P36245
-
-
2.1.1.228 Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412 P36245
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Escherichia coli S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Saccharomyces cerevisiae S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Salmonella enterica subsp. enterica serovar Typhimurium S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Saccharomyces cerevisiae ATCC 204508 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNAPro(UGG)
-
 Escherichia coli S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAPro(UGG)
-
 ?

Synonyms

EC Number Synonyms Comment Organism
2.1.1.228 TrmD
-
 Escherichia coli
2.1.1.228 TrmD
-
 Salmonella enterica subsp. enterica serovar Typhimurium

Cofactor

EC Number Cofactor Comment Organism Structure
2.1.1.228 S-adenosyl-L-methionine
-
 Escherichia coli
2.1.1.228 S-adenosyl-L-methionine
-
 Saccharomyces cerevisiae
2.1.1.228 S-adenosyl-L-methionine
-
 Salmonella enterica subsp. enterica serovar Typhimurium

Expression

EC Number Organism Comment Expression
2.1.1.228 Salmonella enterica subsp. enterica serovar Typhimurium cells expressing the native trmD show more than a 6fold activation of transcription upon switching from high to low Mg2+ media, whereas cells expressing a S88L mutant trmD show less than a 2fold activation. For cells expressing the native trmD, the level of Mg2+ modulates the level of TrmD-dependent m1G37-tRNA synthesis, which in turn modulates the speed of ribosomal translation of m1G37-dependent codons in the 5'-leader ORF. At high Mg2+, TrmD is active and the abundantly synthesized m1G37-tRNA facilitates ribosomal translation through the 5'-leader ORF up

General Information

EC Number General Information Comment Organism
2.1.1.228 evolution in the bacterial domain, the biosynthesis of m1G37 is catalyzed by the tRNA methyltransferase TrmD, whereas in the eukaryotic and archaeal domains, it is catalyzed by Trm5. While both TrmD and Trm5 perform the same methyl transfer reaction, using S-adenosyl methionine (AdoMet) as the methyl donor, they are fundamentally different in structure, where TrmD is a member of the SpoU-TrmD family and Trm5 is a member of the Rossmann-fold family. TrmD and Trm5 also differ in virtually all aspects of the reaction mechanism Escherichia coli
2.1.1.228 evolution in the bacterial domain, the biosynthesis of m1G37 is catalyzed by the tRNA methyltransferase TrmD, whereas in the eukaryotic and archaeal domains, it is catalyzed by Trm5. While both TrmD and Trm5 perform the same methyl transfer reaction, using S-adenosyl methionine (AdoMet) as the methyl donor, they are fundamentally different in structure, where TrmD is a member of the SpoU-TrmD family and Trm5 is a member of the Rossmann-fold family. TrmD and Trm5 also differ in virtually all aspects of the reaction mechanism Saccharomyces cerevisiae
2.1.1.228 evolution in the bacterial domain, the biosynthesis of m1G37 is catalyzed by the tRNA methyltransferase TrmD, whereas in the eukaryotic and archaeal domains, it is catalyzed by Trm5. While both TrmD and Trm5 perform the same methyl transfer reaction, using S-adenosyl methionine (AdoMet) as the methyl donor, they are fundamentally different in structure, where TrmD is a member of the SpoU-TrmD family and Trm5 is a member of the Rossmann-fold family. TrmD and Trm5 also differ in virtually all aspects of the reaction mechanism Salmonella enterica subsp. enterica serovar Typhimurium
2.1.1.228 malfunction Lack of m1G37 promotes the tRNA to make +1-frameshifts in a fast mechanism during tRNA translocation from the A- to the P-site on the ribosome, and also in a much slower mechanism during tRNA stalling on the P-site next to an empty A-site Escherichia coli
2.1.1.228 additional information codon-specific translation in Mg2+ homeostasis, overview. Mg2+ homeostasis in Salmonella is maintained by the membrane-bound two-component system PhoPQ sensing of the external low Mg2+, which activates transcription of the major transporter gene mgtA. Transcription of mgtA is determined by ribosomal translation of the 5'-leader ORF, which contains several m1G37-dependent Pro codons Salmonella enterica subsp. enterica serovar Typhimurium
2.1.1.228 physiological function the N1-methylation of G37 on the 3'-side of the tRNA anticodon, generating m1G37, which as a single methylated nucleobase is not only essential for life but is also conserved in evolution present in all three domains of life. Codon-specific translation by m1G37 methylation of tRNA, mechanism, overview. Maintenance of protein synthesis reading frame by m1G37-tRNA. The maintenance of protein synthesis reading frame in normal cellular conditions is achieved with unexpectedly high fidelity. Due to the dependence on m1G37 for cell survival, Trm5 is required for growth in the single-cell eukaryote Saccharomyces cerevisiae, where it provides the important role of preventing mis-charging of tRNA Saccharomyces cerevisiae
2.1.1.228 physiological function the N1-methylation of G37 on the 3'-side of the tRNA anticodon, generating m1G37, which as a single methylated nucleobase is not only essential for life but is also conserved in evolution present in all three domains of life. Codon-specific translation by m1G37 methylation of tRNA, mechanism, overview. Maintenance of protein synthesis reading frame by m1G37-tRNA. The maintenance of protein synthesis reading frame in normal cellular conditions is achieved with unexpectedly high fidelity. Due to the dependence on m1G37 for cell survival, TrmD is required for growth in several bacterial species, including Escherichia coli and Salmonella Escherichia coli
2.1.1.228 physiological function the N1-methylation of G37 on the 3'-side of the tRNA anticodon, generating m1G37, which as a single methylated nucleobase is not only essential for life but is also conserved in evolution present in all three domains of life. Codon-specific translation by m1G37 methylation of tRNA, mechanism, overview. Maintenance of protein synthesis reading frame by m1G37-tRNA. The maintenance of protein synthesis reading frame in normal cellular conditions is achieved with unexpectedly high fidelity. Due to the dependence on m1G37 for cell survival, TrmD is required for growth in several bacterial species, including Escherichia coli and Salmonella Salmonella enterica subsp. enterica serovar Typhimurium