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Literature summary for 2.1.1.228 extracted from

  • 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) (2013), J. Biol. Chem., 288, 28987-28996.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
gene trmD, recombinant expression of N-terminally His-tagged wild-type and S88L mutant enzymes in Escherichia coli strain SG13009 Escherichia coli

Protein Variants

Protein Variants Comment Organism
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 Escherichia coli

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information Michaelis-Menten steady-state kinetics analysis Escherichia coli
0.0024
-
guanine37 in tRNALeu recombinant wild-type enzyme, pH 8.0, 30°C Escherichia coli
0.0031
-
guanine37 in tRNALeu recombinant wild-type enzyme, pH 8.0, 37°C Escherichia coli
0.013
-
guanine37 in tRNALeu recombinant mutant S88L, pH 8.0, 30°C Escherichia coli
0.0217
-
guanine37 in tRNALeu recombinant wild-type enzyme, pH 8.0, 43°C Escherichia coli
0.0522
-
guanine37 in tRNALeu recombinant mutant S88L, pH 8.0, 37°C Escherichia coli
0.0625
-
guanine37 in tRNALeu recombinant mutant S88L, pH 8.0, 43°C Escherichia coli

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
S-adenosyl-L-methionine + guanine37 in tRNA Escherichia coli
-
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
?

Organism

Organism UniProt Comment Textmining
Escherichia coli P0A873 gene trmD
-

Purification (Commentary)

Purification (Comment) Organism
recombinant N-terminally His-tagged wild-type and S88L mutant enzymes from Escherichia coli strain SG13009 by nickel affinity chromatography Escherichia coli

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
S-adenosyl-L-methionine + guanine37 in tRNA
-
Escherichia coli S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
?
S-adenosyl-L-methionine + guanine37 in tRNALeu
-
Escherichia coli S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNALeu
-
?
S-adenosyl-L-methionine + guanine37 in tRNAPro the A37 mutant of EctRNAPro is no substrate for the enzyme Escherichia coli S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAPro
-
?

Subunits

Subunits Comment Organism
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 Escherichia coli

Synonyms

Synonyms Comment Organism
TrmD
-
Escherichia coli
tRNA methyltransferase D
-
Escherichia coli

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
30 43 assay at Escherichia coli

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.0015
-
guanine37 in tRNALeu recombinant mutant S88L, pH 8.0, 43°C Escherichia coli
0.0032
-
guanine37 in tRNALeu recombinant mutant S88L, pH 8.0, 30°C Escherichia coli
0.0067
-
guanine37 in tRNALeu recombinant mutant S88L, pH 8.0, 37°C Escherichia coli
0.049
-
guanine37 in tRNALeu recombinant wild-type enzyme, pH 8.0, 30°C Escherichia coli
0.093
-
guanine37 in tRNALeu recombinant wild-type enzyme, pH 8.0, 37°C Escherichia coli
0.13
-
guanine37 in tRNALeu recombinant wild-type enzyme, pH 8.0, 43°C Escherichia coli

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8
-
assay at Escherichia coli

Cofactor

Cofactor Comment Organism Structure
S-adenosyl-L-methionine
-
Escherichia coli

General Information

General Information Comment Organism
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 Escherichia coli
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 Escherichia coli

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.024
-
guanine37 in tRNALeu recombinant mutant S88L, pH 8.0, 43°C Escherichia coli
0.13
-
guanine37 in tRNALeu recombinant mutant S88L, pH 8.0, 37°C Escherichia coli
0.25
-
guanine37 in tRNALeu recombinant mutant S88L, pH 8.0, 30°C Escherichia coli
5.99
-
guanine37 in tRNALeu recombinant wild-type enzyme, pH 8.0, 43°C Escherichia coli
20.42
-
guanine37 in tRNALeu recombinant wild-type enzyme, pH 8.0, 30°C Escherichia coli
30
-
guanine37 in tRNALeu recombinant wild-type enzyme, pH 8.0, 37°C Escherichia coli