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Information on EC 2.1.1.228 - tRNA (guanine37-N1)-methyltransferase and Organism(s) Escherichia coli and UniProt Accession P0A873
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2.1.1.228 tRNA (guanine37-N1)-methyltransferaseIUBMB Comments
This enzyme is important for the maintenance of the correct reading frame during translation. Unlike TrmD from Escherichia coli, which recognizes the G36pG37 motif preferentially, the human enzyme (encoded by TRMT5) also methylates inosine at position 37 .
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Word Map
- 2.1.1.228
- methyltransferases
-
anticodon
- adomet
- 1-methylguanosine
- drug development
-
n2-guanine
- trmt10a
- 1-methyladenine
-
adomet-dependent
- 5-methyluridine
- trmfo
-
n1-methylation
-
methyl-deficient
- 7-methylguanine
-
spout
-
epitranscriptome
-
nsun2-mediated
- medicine
The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
+
guanine37 in tRNA
=
+
N1-methylguanine37 in tRNA
Synonyms
trna methyltransferase, trna(m1g37)methyltransferase, patrmd, trna(m(1)g37)methyltransferase, trm5p, patrm5a, trna (m1g37) methyltransferase, trmt5, attrm5a, trna (guanosine-1) methyltransferase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + guanine37 in tRNA = S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
S-adenosyl-L-methionine + guanine37 in tRNA = S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
substrate recognition and reaction mechanisms, overview
-
S-adenosyl-L-methionine + guanine37 in tRNA = S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
catalytic mechanism in which the role of Mg2+ is to help to increase the nucleophilicity of N1 of G37 and stabilize the negative developing charge on O6 during attack on the methyl sulfonium of S-adenosyl-L-methionine. Substrate binding to EcTrmD is in rapid equilibrium to form the enzyme-tRNA-S-adenosyl-L-methionine complex, a proton abstraction step is rate limiting in methyl transfer
-
PATHWAY SOURCE
PATHWAYS
-
-, -, -
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:tRNA (guanine37-N1)-methyltransferase
This enzyme is important for the maintenance of the correct reading frame during translation. Unlike TrmD from Escherichia coli, which recognizes the G36pG37 motif preferentially, the human enzyme (encoded by TRMT5) also methylates inosine at position 37 [4].
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + guanine37 in Escherichia coli tRNA1Leu
S-adenosyl-L-homocysteine + N1-methylguanine37 in Escherichia coli tRNA1Leu
-
-
-
?
S-adenosyl-L-methionine + guanine37 in human mitochondrial tRNAPro
S-adenosyl-L-homocysteine + N1-methylguanine37 in human mitochondrial tRNAPro
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
S-adenosyl-L-methionine + guanine37 in tRNALeu
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNALeu
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAPro
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAPro
the A37 mutant of EctRNAPro is no substrate for the enzyme
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAPro(UGG)
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAPro(UGG)
-
-
-
?
S-adenosyl-L-methionine + guanine37 in yeast tRNAAsp possessing a G36G37 sequence
S-adenosyl-L-homocysteine + N1-methylguanine37 in yeast tRNAAsp possessing a G36G37 sequence
-
-
-
?
S-adenosyl-L-methionine + guanine37 in yeast tRNAAsp possessing an A36G37 sequence
S-adenosyl-L-homocysteine + N1-methylguanine37 in yeast tRNAAsp possessing an A36G37 sequence
-
-
-
?
S-adenosyl-L-methionine + guanine36 in tRNALeu
S-adenosyl-L-homocysteine + N1-methylguanine36 in tRNALeu
-
G36-substituted tRNA substrate Escherichia coli tRNALeu, TrmD shows a 90fold reduced catalytic efficiency, discrimination between the two sequences of G36 and G37
-
-
?
S-adenosyl-L-methionine + guanine37 in Escherichia coli tRNAPro
S-adenosyl-L-homocysteine + N1-methylguanine37 in Escherichia coli tRNAPro
-
-
-
-
?
S-adenosyl-L-methionine + guanine37 in Methanocaldococcus jannaschii tRNAPro
S-adenosyl-L-homocysteine + N1-methylguanine37 in Methanocaldococcus jannaschii tRNAPro
-
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
S-adenosyl-L-methionine + guanine37 in tRNALeu
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNALeu
-
Escherichia coli tRNALeu
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
methylates the N1 position of guanosine 37 (G37) in selected tRNA transcripts
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
substrate binding stoichiometry to TrmD, dissociation constants, overview
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
TrmD recognizes N1 and O6 of G37 and the exocyclic 2-amino group of G37 is important for TrmD, also TrmD requires G36 for synthesis of m1G37
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
the pH-activity profile indicates one proton transfer during the TrmD reaction
-
-
?
additional information
?
-
TrmD recognizes the G36pG37 motif preferentially and does not methylate inosine. The TrmD enzyme is tolerant of alterations in tRNA-protein tertiary interactions as long as the core tRNA structure and the G36pG37 are present
-
-
?
additional information
?
-
-
TrmD recognizes the G36pG37 motif preferentially and does not methylate inosine. The TrmD enzyme is tolerant of alterations in tRNA-protein tertiary interactions as long as the core tRNA structure and the G36pG37 are present
-
-
?
additional information
?
-
TrmD synthesizes the methylated m1G37 on bacterial tRNAs that contain both G37 and a preceding G36, the 3'-nucleotide of the anticodon
-
-
-
additional information
?
-
proposed model for the TrmD enzymatic cycle which consists of the AdoMet-binding, tRNA-binding, and methyl transfer stages, overview. Anticodon-branch recognition and detection of position 37, interaction analysis of TrmD with G36 and G37
-
-
-
additional information
?
-
radioactive assay method development and evaluation using labeled S-adenosyl-L-methionine and unlabeled tRNA, detailed overview. The slow step of the TrmD reaction is the chemistry of methyl transfer
-
-
-
additional information
?
-
TrmD can methylate a truncated tRNA, in which T- and D-arms have been deleted, the anticodon-arm region is mainly protected
-
-
-
additional information
?
-
-
TrmD catalyzes methyl transfer to synthesize the m1G37 base at the 3' position adjacent to the tRNA anticodon
-
-
?
additional information
?
-
-
recognition of N1 of G37 in tRNA is essential for translational fidelity in all biological domains, TrmD shows a more rigid requirement of guanosine functional groups. Replacment of functional groups of G37 by guanosine analogues, i.e. deoxyG, 6-thioG, inosine, and 2-aminopurine, in EctRNALeu, to design the optimal substrate for TrmD. All but deoxyG of these analogs probed the Watson-Crick basepairing interface of G37
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
S-adenosyl-L-methionine + guanine37 in tRNAPro(UGG)
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAPro(UGG)
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
?
additional information
?
-
TrmD synthesizes the methylated m1G37 on bacterial tRNAs that contain both G37 and a preceding G36, the 3'-nucleotide of the anticodon
-
-
-
additional information
?
-
-
TrmD catalyzes methyl transfer to synthesize the m1G37 base at the 3' position adjacent to the tRNA anticodon
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mg2+
-
dependent on, one Mg2+ per enzyme dimer. Mg2+ is not involved in substrate binding, but in promoting methyl transfer. Mg2+ promotes methyl transfer of TrmD not by stabilizing the binding of tRNA or AdoMet, but by accelerating the chemical rate. Mg2+ interacts with the O6 of G37-tRNA
additional information
Mg2+
methyl transfer by TrmD requires Mg2+ in the catalytic mechanism, kinetics
additional information
in addition to Mg2+, TrmD can also use Ca2+ and Mn2+ as an active ion, but not Ni2+ or Co2+. The single Mg2+ required for methyl transfer is involved in the abstraction of the N1 proton from G37-tRNA, which is likely the rate-limiting step of the TrmD-catalyzed methyl transfer
additional information
-
bacterial enzyme TrmD is strongly dependent on divalent metal ions and Mg2+ is the most physiologically relevant. Divalent metal ions are recruited to stabilize the developing negative charge at the 6-position of G37, while also favoring the abstraction of the N1 proton to activate the nucleophile. Co2+ is unable to substitute for Mg2+, replacement of Mg2+ with Co2+ decreases methyl transfer, substitution of the 6-oxygen (O6) of G37 with 6-thio (S6) in the substrate tRNA restores the activity. Kinetics of metal ions in the reaction,overview
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
DTT
TrmD has maximal activity below 1 mM DTT and loses 20% of its activity above that value
glycerol
the Escherichia coli TRmD performs best in the absence of glycerol, its activity decresaing linearly with increasing glycerol concentrations. No activity at 50% glycerol
additional information
-
fragments of S-adenosyl-L-methionine, adenosine and methionine, are selectively inhibitory of TrmD, while they are poor inhibitors for Trm5 from Methanocaldococcus jannaschii
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.019
guanine37 in yeast tRNAAsp possessing a G36G37 sequence
pH 8.0, 37°C
-
0.046
guanine37 in yeast tRNAAsp possessing an A36G37 sequence
pH 8.0, 37°C
-
0.0024
guanine37 in tRNALeu
recombinant wild-type enzyme, pH 8.0, 30°C
-
0.0031
guanine37 in tRNALeu
recombinant wild-type enzyme, pH 8.0, 37°C
-
0.0217
guanine37 in tRNALeu
recombinant wild-type enzyme, pH 8.0, 43°C
-
additional information
additional information
Michaelis-Menten kinetic analysis
-
additional information
additional information
Michaelis-Menten steady-state kinetics analysis
-
additional information
additional information
-
Michaelis-Menten steady-state kinetics analysis
-
additional information
additional information
pre-steady-state and steady-state Michaelis-Menten kinetics, single turnover assays
-
additional information
additional information
-
kinetic analysis of tRNA truncation mutants and tRNA mutant with alterations in the anticodon loop reveals that TrmD and Trm5 exhibit separate and distinct mode of tRNA recognition, suggesting that they evolved by independent and nonoverlapping pathways from their unrelated AdoMet families
-
additional information
additional information
-
pre-steady-state and steady-state kinetics, time-dependent linear reaction, overview. TrmD exhibits half-of-the-sites reactivity in which only one of the two active sites is functional at a given time
-
additional information
additional information
-
S-adenosyl-L-methionine and adenosine binding kinetics and kinetic analysis of enzyme reaction, overview
-
additional information
additional information
-
single turnover kinetics and thermodynamic analysis of effect of different guanosine analogues on m1G37-tRNA synthesis, kinetic analysis, overview
-
additional information
additional information
-
measurement of the pre-steady-state rate constant of methyl transfer of TrmD, a proton abstraction step is rate limiting, steady-state kinetics
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.09
S-adenosyl-L-methionine
-
pH and temperature not specified in the publication
additional information
additional information
-
kinetic analysis of tRNA truncation mutants and tRNA mutant with alterations in the anticodon loop reveals that TrmD and Trm5 exhibit separate and distinct mode of tRNA recognition, suggesting that they evolved by independent and nonoverlapping pathways from their unrelated AdoMet families
-
0.049
guanine37 in tRNALeu
recombinant wild-type enzyme, pH 8.0, 30°C
-
0.093
guanine37 in tRNALeu
recombinant wild-type enzyme, pH 8.0, 37°C
-
0.13
guanine37 in tRNALeu
recombinant wild-type enzyme, pH 8.0, 43°C
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
kinetic analysis of tRNA truncation mutants and tRNA mutant with alterations in the anticodon loop reveals that TrmD and Trm5 exhibit separate and distinct mode of tRNA recognition, suggesting that they evolved by independent and nonoverlapping pathways from their unrelated AdoMet families
-
5.99
guanine37 in tRNALeu
recombinant wild-type enzyme, pH 8.0, 43°C
-
20.42
guanine37 in tRNALeu
recombinant wild-type enzyme, pH 8.0, 30°C
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.01
5'-[(2-aminoethyl)thio]-5'-deoxy-adenosine
-
pH not specified in the publication, 37°C
0.0042
S-adenosyl-L-homocysteine
-
pH not specified in the publication, 37°C
additional information
additional information
-
inhibition kinetics of S-adenosyl-L-methionine analogues, overview
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
physiological function
evolution
-
the dedication of Mg2+ to rate enhancement separates TrmD from O- and N6-methyl transferases. TrmD shows the topologically knotted protein fold
physiological function
additional information
evolution
at least 5 classes (class I-V) of structurally distinct AdoMet-dependent methyltransferases have been identified. TrmD belongs to the class IV tRNA methyl transferases. TrmD is an obligated dimer that uses the class IV-fold for AdoMet binding. EcTrmD is homologous to Haemophilus influenza TrmD
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
evolution
the enzyme TrmD belongs to the 2'-O-methyltransferase family, previously SpoU family of enzymes, conserved motifs in the TrmH (SpoU) and TrmD families, overview. Comparisons of topological knot structures in TrmH (SpoU) and TrmD. AdoMet-dependent enzymes can be divided into more than five classes according to the structure of their catalytic domain. Most methyltransferases have a Rossman fold catalytic domain and are classified as class I enzymes. In contrast, members of SPOUT RNA methyltransferase superfamily are classified as class IV enzymes, whose catalytic domain forms a deep trefoil (topological) knot. TrmD from Escherichia coli belongs to the m1G37 methyltransferases
evolution
the N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. Enzyme structure and function analysis and comparisons of Pyrococcus abyssi and Methanocaldococcus jannaschii Trm5 enzymes with Escherichia coli and Haemophilus influenzae TrmD enzymes, overview. TrmD requires not only G37 but also G36 as a substrate tRNA sequence, and the nine-base pair RNA duplex consisting of the anticodon and D stems with the anticodon loop can serve as its minimum substrate. In contrast, Trm5 requires G37 together with the entire tRNA structure. Enzyme TrmD belongs to the class IV methyltransferases.
evolution
TrmD is broadly conserved in sequence and structure among bacterial species, in both Gram (+) and Gram (-), but it is absent from the eukaryotic and archaeal domains. TrmD is strongly conserved in sequence among evolutionarily diverse bacterial species. In all of the available structures of the TrmD dimer, each monomeric chain is made up of three distinct domains: an N-terminal domain (residues 1-160 in HiTrmD and EcTrmD) for binding AdoMet, a C-terminal domain for binding tRNA (residues 169-246), and a flexible linker in between (residues 161-168)
malfunction
the ts phenotype of an essential gene mutation S88L in gene trmD can be closely linked to the catalytic defect of the gene product
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
malfunction
mutations in the TrmD knot block this intramolecular signaling and decrease the synthesis of m1G37-tRNA, prompting ribosomes to +1-frameshifts and premature termination of protein synthesis. Ribosome frameshifting in the absence of TrmD, overview
physiological function
enzyme TrmD catalyzes the transfer of methyl group from AdoMet to N1-atom of G37 in tRNA to form m1G37
physiological function
he N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome
physiological function
methylation is to the G37 base on the 3' side of the anticodon to generate m1G37-tRNA suppresses frameshift errors during protein synthesis and is therefore essential for cell growth in all three domains of life. This methylation is catalyzed by TrmD in bacteria and by Trm5 in eukaryotes and archaea. Although TrmD and Trm5 catalyze the same methylation reaction, kinetic analysis reveal that these two enzymes are unrelated to each other and are distinct in their reaction mechanism. Both TrmD and Trm5 are essential for cell growth, because their reaction product m1G37 occurring on the 3' side of the tRNA anticodon is necessary to suppress +1-frameshift errors on the ribosome
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
physiological function
while the greatest majority of the tRNA modifying enzymes are nonessential for life, acting for example as a chaperone to modulate tRNA activity, a very small number of these enzymes are absolutely required for cell growth and survival. TrmD is an example of one of these essential enzymes, responsible for methyl transfer from AdoMet to the N1 position of the G37 base to synthesize m1G37 on tRNA. TrmD is an S-adenosyl methionine (AdoMet)-dependent methyl transferase that synthesizes the methylated m1G37 in tRNA. TrmD is specific to and essential for bacterial growth, and it is fundamentally distinct from its eukaryotic and archaeal counterpart Trm5. TrmD is unusual by using a topological protein knot to bind AdoMet. Despite its restricted mobility, the TrmD knot has complex dynamics necessary to transmit the signal of AdoMet binding to promote tRNA binding and methyl transfer. TrmD is unique among AdoMet-dependent methyl transferases in that it requires Mg2+ in the catalytic mechanism. The trefoil knot of TrmD is required for the catalytic mechanism in three ways. Synthesis of m1G37-tRNA by TrmD is a posttranscriptional event
physiological function
-
the m1G37 modification prevents tRNA frameshifts on the ribosome by assuring correct codon-anticodon pairings, and thus is essential for the fidelity of protein synthesis
physiological function
-
S-adenosyl-L-methionine-dependent methyl transfer in one of the most crucial posttranscriptional modifications to tRNA
additional information
in the cross-subunit active site, S-adenosyl-L-methionine is bound to the trefoil knot fold in the N-terminal domain, whereas the target G37 is predicted to bind to the flexible linker
additional information
-
in the cross-subunit active site, S-adenosyl-L-methionine is bound to the trefoil knot fold in the N-terminal domain, whereas the target G37 is predicted to bind to the flexible linker
additional information
evaluation of the kinetic assays that are used to reveal the distinction between TrmD and Trm5, overview
additional information
the m1G37 methylation by TrmD does not need any other prior modification, aminoacylation, or even CCA addition to tRNA. Transient nature of Mg2+ is consistent with the proposed catalytic mechanism involving G37-tRNA. In this mechanism, D169 is the general base to abstract the N1 proton from G37, while the deprotonation is accompanied by developing electron density on the O6 of G37. The developing negative charge on O6 of G37 is stabilized through coordination with Mg2+ and by hydrogen-bond interaction with the side chain of R154. The charge stabilization of O6 in turn facilitates Mg2+ to coordinate with the general base D169 and to help it to align more properly for proton abstraction. The activated N1 nucleophile is then poised for nucleophilic attack on the sulfonium center of AdoMet, resulting in synthesis of m1G37-tRNA and release of AdoHcy. The rate-limiting step is assigned to the action of D169, rather than to the protonation of the leaving group, due to the importance of D169 and the increase of activity as the proton concentration is lowered
additional information
TrmD consists of the N-terminal domain (NTD, the SPOUT domain) and the TrmD-specific C-terminal domain (CTD). These domains are connected by the interdomain linker. TrmD forms a homodimer, and the interdomain linkers are disordered in both monomers. The trefoil knot at the C-terminal region in the SPOUT domain provides the AdoMet-binding site. Structural changes of TrmD upon AdoMet accommodation. Structure-function analysis, overview
additional information
-
S-adenosyl-methionine-dependent m1G37-tRNA methyltransferases rapidly screen tRNA by direct recognition of G37 in order to monitor the global state of m1G37-tRNA
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
homodimer
TrmD exists as an obligate homodimer, with each subunit featuring an N-terminal domain (residues 1-159), a flexible linker (residues 160-169), and a C-terminal domain (residues 170-250), the active site is built between the N-terminal domain of one subunit and the flexible linker and the C-terminal domain of the other
dimer
additional information
dimer
each monomer consists of a C-terminal domain connected by a flexible linker to an N-terminal AdoMet-binding domain
dimer
TrmD is an obligated homodimer that places each active site at the dimer interface
additional information
in both monomeric chains of TrmD, AdoMet is bound in the N-terminal domain to the deep cleft of a trefoil knot fold, which is a topological knot that involves three crossings of the protein backbone through a loop, the trefoil knot in TrmD is shown to be required for methyl transfer, knot structure and function, overview. The trefoil knot of TrmD is required for the catalytic mechanism in three ways
additional information
knot structures, domain arrangements, subunit structures and reaction mechanisms of tRNA methyltransferases with a SPOUT fold, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of TrmD complexed with S-adenosyl homocysteine, determined at 2.5 A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
S88L
naturally occuring mutation of trmD, the mutation confers thermal lability to the enzyme with a minor effect. The mutation decreases the catalytic efficiency of the enzyme to 1% of wild-type activity at permissive temperature. At nonpermissive temperature, it renders further deterioration of activity to 0.1%. These changes are accompanied by losses of both the quantity and quality of tRNA methylation, leading to the potential of cellular pleiotropic effects
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant N-terminally His-tagged wild-type and S88L mutant enzymes from Escherichia coli strain SG13009 by nickel affinity chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene trmD, recombinant expression of N-terminally His-tagged wild-type and S88L mutant enzymes in Escherichia coli strain SG13009
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
TrmD is ranked as a high-priority antimicrobial target
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Brule, H.; Elliott, M.; Redlak, M.; Zehner, Z.E.; Holmes, W.M.
Isolation and characterization of the human tRNA-(N1G37) methyltransferase (TRM5) and comparison to the Escherichia coli TrmD protein
Biochemistry
43
9243-9255
2004
Escherichia coli (P0A873), Escherichia coli, Homo sapiens (Q32P41), Homo sapiens
Elkins, P.A.; Watts, J.M.; Zalacain, M.; van Thiel, A.; Vitazka, P.R.; Redlak, M.; Andraos-Selim, C.; Rastinejad, F.; Holmes, W.M.
Insights into catalysis by a knotted TrmD tRNA methyltransferase
J. Mol. Biol.
333
931-949
2003
Escherichia coli (P0A873), Escherichia coli
Christian, T.; Hou, Y.M.
Distinct determinants of tRNA recognition by the TrmD and Trm5 methyl transferases
J. Mol. Biol.
373
623-632
2007
Escherichia coli, Methanocaldococcus jannaschii (Q58293)
Christian, T.; Lahoud, G.; Liu, C.; Hou, Y.M.
Control of catalytic cycle by a pair of analogous tRNA modification enzymes
J. Mol. Biol.
400
204-217
2010
Escherichia coli, Methanocaldococcus jannaschii
Lahoud, G.; Goto-Ito, S.; Yoshida, K.; Ito, T.; Yokoyama, S.; Hou, Y.M.
Differentiating analogous tRNA methyltransferases by fragments of the methyl donor
RNA
17
1236-1246
2011
Escherichia coli, Methanocaldococcus jannaschii
Sakaguchi, R.; Giessing, A.; Dai, Q.; Lahoud, G.; Liutkeviciute, Z.; Klimasauskas, S.; Piccirilli, J.; Kirpekar, F.; Hou, Y.M.
Recognition of guanosine by dissimilar tRNA methyltransferases
RNA
18
1687-1701
2012
Escherichia coli, Methanocaldococcus jannaschii
Sakaguchi, R.; Lahoud, G.; Christian, T.; Gamper, H.; Hou, Y.M.
A divalent metal ion-dependent N1-methyl transfer to G37-tRNA
Chem. Biol.
21
1351-1360
2014
Escherichia coli
Masuda, I.; Sakaguchi, R.; Liu, C.; Gamper, H.; Hou, Y.M.
The temperature sensitivity of a mutation in the essential tRNA modification enzyme tRNA methyltransferase D (TrmD)
J. Biol. Chem.
288
28987-28996
2013
Escherichia coli (P0A873), Escherichia coli
Goto-Ito, S.; Ito, T.; Yokoyama, S.
Trm5 and TrmD two enzymes from distinct origins catalyze the identical tRNA modification, m1G37
Biomolecules
7
32
2017
Escherichia coli (P0A873), Haemophilus influenzae (P43912), Haemophilus influenzae ATCC 51907 (P43912), Haemophilus influenzae DSM 11121 (P43912), Haemophilus influenzae KW20 (P43912), Haemophilus influenzae RD (P43912), Methanocaldococcus jannaschii (Q58293), Methanocaldococcus jannaschii ATCC 43067 (Q58293), Methanocaldococcus jannaschii DSM 2661 (Q58293), Methanocaldococcus jannaschii JAL-1 (Q58293), Methanocaldococcus jannaschii JCM 10045 (Q58293), Methanocaldococcus jannaschii NBRC 100440 (Q58293), Pyrococcus abyssi (Q9V2G1), Pyrococcus abyssi Orsay (Q9V2G1)
Hori, H.
Transfer RNA methyltransferases with a SpoU-TrmD (SPOUT) fold and their modified nucleosides in tRNA
Biomolecules
7
E23
2017
Haemophilus influenzae (A0A0D0GZF5), Aquifex aeolicus (O67463), Escherichia coli (P0A873)
Hou, Y.; Matsubara, R.; Takase, R.; Masuda, I.; Sulkowska, J.
TrmD A methyl transferase for tRNA methylation with m1G37
Enzymes
41
89-115
2017
Haemophilus influenzae (A0A0D0GZF5), Aquifex aeolicus (O67463), Escherichia coli (P0A873), Salmonella enterica subsp. enterica serovar Typhimurium (P36245), Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412 (P36245), Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720 (P36245)
Hou, Y.; Masuda, I.; Gamper, H.
Codon-specific translation by m1G37 methylation of tRNA
Front. Genet.
10
713
2019
Escherichia coli (P0A873), Salmonella enterica subsp. enterica serovar Typhimurium (P36245), Saccharomyces cerevisiae (P38793), Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412 (P36245), Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720 (P36245), Saccharomyces cerevisiae ATCC 204508 (P38793)
Hou, Y.M.; Masuda, I.
Kinetic analysis of tRNA methyltransferases
Methods Enzymol.
560
91-116
2015
Escherichia coli (P0A873), Haemophilus influenzae (P43912), Haemophilus influenzae ATCC 51907 (P43912), Haemophilus influenzae DSM 11121 (P43912), Haemophilus influenzae KW20 (P43912), Haemophilus influenzae RD (P43912), Homo sapiens (Q32P41), Methanocaldococcus jannaschii (Q58293), Methanocaldococcus jannaschii ATCC 43067 (Q58293), Methanocaldococcus jannaschii DSM 2661 (Q58293), Methanocaldococcus jannaschii JAL-1 (Q58293), Methanocaldococcus jannaschii JCM 10045 (Q58293), Methanocaldococcus jannaschii NBRC 100440 (Q58293)
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