Literature summary for 2.1.1.228 extracted from

Ito, T.; Masuda, I.; Yoshida, K.; Goto-Ito, S.; Sekine, S.; Suh, S.W.; Hou, Y.M.; Yokoyama, S.
Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD (2015), Proc. Natl. Acad. Sci. USA, 112, E4197-E4205.

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Crystallization (Commentary)

Crystallization (Comment)	Organism
purified enzyme in complex with Thermotoga maritima wild-type and mutant tRNA substrates, e.g. tRNAGlnCUG, and the S-adenosyl-L-methionine analogue sinefungin, X-ray crystal structure analysis, PDB ID 3AKZ	Thermotoga maritima
purified enzyme in ternary complex with Thermotoga maritima wild-type and mutant tRNA substrates, e.g. tRNAGlnCUG, and the S-adenosyl-L-methionine analogue sinefungin, and enzyme in TrmD-AdoMet and TrmD-sinefungin binary complexes, 0.0012 ml of 10 mg/ml protein and 1 mM AdoMet or sinefungin, is mixed with 0.0012 ml of reservoir solution, consisting of 0.8-0.85 M sodium citrate and 0.1 M N-cyclohexyl-2-minoethanesulfonic acid, pH 8.0-8.4, 20°C, for the trinary complex 5 mg/ml protein is mixed with tRNA in a 5:1 ratio, and 1 mM sinefungin, 0.0012 ml are mixed with 0.0015 ml of reservoir solution containing 0.1 M sodium acetate trihydrate, pH 4.6, 0.8 M ammonium phosphate monobasic, and 4% w/v PEG 20,000, X-ray diffraction structure determination and analysis at 3.0 A, 1.55 A, and 1.6 A resolutions, respectively, structure modeling	Haemophilus influenzae

Crystallization (Comment)

Organism

purified enzyme in complex with Thermotoga maritima wild-type and mutant tRNA substrates, e.g. tRNAGlnCUG, and the S-adenosyl-L-methionine analogue sinefungin, X-ray crystal structure analysis, PDB ID 3AKZ

Thermotoga maritima

purified enzyme in ternary complex with Thermotoga maritima wild-type and mutant tRNA substrates, e.g. tRNAGlnCUG, and the S-adenosyl-L-methionine analogue sinefungin, and enzyme in TrmD-AdoMet and TrmD-sinefungin binary complexes, 0.0012 ml of 10 mg/ml protein and 1 mM AdoMet or sinefungin, is mixed with 0.0012 ml of reservoir solution, consisting of 0.8-0.85 M sodium citrate and 0.1 M N-cyclohexyl-2-minoethanesulfonic acid, pH 8.0-8.4, 20°C, for the trinary complex 5 mg/ml protein is mixed with tRNA in a 5:1 ratio, and 1 mM sinefungin, 0.0012 ml are mixed with 0.0015 ml of reservoir solution containing 0.1 M sodium acetate trihydrate, pH 4.6, 0.8 M ammonium phosphate monobasic, and 4% w/v PEG 20,000, X-ray diffraction structure determination and analysis at 3.0 A, 1.55 A, and 1.6 A resolutions, respectively, structure modeling

Haemophilus influenzae

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
additional information	-	additional information	structure-guided kinetic analysis of TrmD mutants and tRNA variants, overview	Haemophilus influenzae
additional information	-	additional information	structure-guided kinetic analysis of TrmD mutants and tRNA variants, overview	Thermotoga maritima
0.00082	-	guanine37 in tRNAGlnCUG	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.001	-	guanine37 in tRNAPro	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.0027	-	guanine37 in tRNAGlnG36A	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.0044	-	guanine37 in tRNAGlnCUG	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.008	-	guanine37 in tRNALeu	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.027	-	guanine37 in tRNAArg	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.064	-	guanine37 in tRNAGlnCUG	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.067	-	guanine37 in tRNAGlnCUG	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.114	-	guanine37 in tRNAGlnG36U	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.184	-	guanine37 in tRNAGlnG36C	pH 8.0, temperature not specified in the publication	Haemophilus influenzae

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
S-adenosyl-L-methionine + guanine37 in tRNA	Haemophilus influenzae	TrmD catalyzes the N1-methylguanosine (m1G) modification at position 37 in tRNAs with the 36GG37 sequence, using S-adenosyl-L-methionine as the methyl donor	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	Thermotoga maritima	TrmD catalyzes the N1-methylguanosine (m1G) modification at position 37 in tRNAs with the 36GG37 sequence, using S-adenosyl-L-methionine as the methyl donor	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	Haemophilus influenzae DSM 11121	TrmD catalyzes the N1-methylguanosine (m1G) modification at position 37 in tRNAs with the 36GG37 sequence, using S-adenosyl-L-methionine as the methyl donor	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?

Organism

Organism	UniProt	Comment	Textmining
Haemophilus influenzae	-	gene trmD	-
Haemophilus influenzae DSM 11121	-	gene trmD	-
Thermotoga maritima	-	gene trmD	-

Reaction

Reaction	Comment	Organism	Reaction ID
S-adenosyl-L-methionine + guanine37 in tRNA = S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	mechanism by which TrmD binds the substrate tRNA in an S-adenosyl-L-methionine-dependent manner: The trefoil-knot center, which is structurally conserved among SPOUTMTases, accommodates the adenosine moiety of S-adenosyl-L-methionine by loosening/retightening of the knot. The TrmD-specific regions surrounding the trefoil knot recognize the methionine moiety of S-adenosyl-L-methionine, and thereby establish the entire TrmD structure for global interactions with tRNA and sequential and specific accommodations of G37 and G36, resulting in the synthesis of m1G37-tRNA	Haemophilus influenzae	a
S-adenosyl-L-methionine + guanine37 in tRNA = S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	mechanism by which TrmD binds the substrate tRNA in an S-adenosyl-L-methionine-dependent manner: The trefoil-knot center, which is structurally conserved among SPOUTMTases, accommodates the adenosine moiety of S-adenosyl-L-methionine by loosening/retightening of the knot. The TrmD-specific regions surrounding the trefoil knot recognize the methionine moiety of S-adenosyl-L-methionine, and thereby establish the entire TrmD structure for global interactions with tRNA and sequential and specific accommodations of G37 and G36, resulting in the synthesis of m1G37-tRNA	Thermotoga maritima	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
S-adenosyl-L-methionine + guanine37 in tRNA	-	Haemophilus influenzae	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	-	Thermotoga maritima	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	TrmD catalyzes the N1-methylguanosine (m1G) modification at position 37 in tRNAs with the 36GG37 sequence, using S-adenosyl-L-methionine as the methyl donor	Haemophilus influenzae	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	TrmD catalyzes the N1-methylguanosine (m1G) modification at position 37 in tRNAs with the 36GG37 sequence, using S-adenosyl-L-methionine as the methyl donor	Thermotoga maritima	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	-	Haemophilus influenzae DSM 11121	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNA	TrmD catalyzes the N1-methylguanosine (m1G) modification at position 37 in tRNAs with the 36GG37 sequence, using S-adenosyl-L-methionine as the methyl donor	Haemophilus influenzae DSM 11121	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA	-	?
S-adenosyl-L-methionine + guanine37 in tRNAArg	tRNA substrate from Haemophilus influenzae	Haemophilus influenzae	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAArg	-	?
S-adenosyl-L-methionine + guanine37 in tRNAArg	tRNA substrate from Haemophilus influenzae	Haemophilus influenzae DSM 11121	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAArg	-	?
S-adenosyl-L-methionine + guanine37 in tRNAGlnCUG	-	Thermotoga maritima	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAGlnCUG	-	?
S-adenosyl-L-methionine + guanine37 in tRNAGlnCUG	the wild-type Thermotoga maritima tRNAGlnCUG transcript is methylated by Haemophilus influenzae TrmD 2.2 to 99fold more efficiently than the Haemophilus influenzae tRNA transcripts	Haemophilus influenzae	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAGlnCUG	-	?
S-adenosyl-L-methionine + guanine37 in tRNAGlnCUG	the wild-type Thermotoga maritima tRNAGlnCUG transcript is methylated by Haemophilus influenzae TrmD 2.2 to 99fold more efficiently than the Haemophilus influenzae tRNA transcripts	Haemophilus influenzae DSM 11121	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAGlnCUG	-	?
S-adenosyl-L-methionine + guanine37 in tRNAGlnG36A	tRNA substrate from Thermotoga maritima	Haemophilus influenzae	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAGlnG36A	-	?
S-adenosyl-L-methionine + guanine37 in tRNAGlnG36C	tRNA substrate from Thermotoga maritima	Haemophilus influenzae	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAGlnG36C	-	?
S-adenosyl-L-methionine + guanine37 in tRNAGlnG36U	tRNA substrate from Thermotoga maritima	Haemophilus influenzae	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAGlnG36U	-	?
S-adenosyl-L-methionine + guanine37 in tRNALeu	tRNA substrate from Haemophilus influenzae	Haemophilus influenzae	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNALeu	-	?
S-adenosyl-L-methionine + guanine37 in tRNALeu	tRNA substrate from Haemophilus influenzae	Haemophilus influenzae DSM 11121	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNALeu	-	?
S-adenosyl-L-methionine + guanine37 in tRNAPro	tRNA substrate from Haemophilus influenzae	Haemophilus influenzae	S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAPro	-	?

Subunits

Subunits	Comment	Organism
homodimer	-	Thermotoga maritima
homodimer	enzyme TrmD consists of the N-terminal domain (residues 1-160) and the C-terminal domain (residues 169-246), and the interdomain linker of residues 161-168 is disordered in the tRNA-free structures	Haemophilus influenzae

Synonyms

Synonyms	Comment	Organism
TrmD	-	Haemophilus influenzae
TrmD	-	Thermotoga maritima

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
0.0014	-	guanine37 in tRNAGlnCUG	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.0047	-	guanine37 in tRNAGlnCUG	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.078	-	guanine37 in tRNAArg	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.13	-	guanine37 in tRNAPro	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.17	-	guanine37 in tRNAGlnG36U	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.24	-	guanine37 in tRNAGlnCUG	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.32	-	guanine37 in tRNALeu	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.34	-	guanine37 in tRNAGlnCUG	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.36	-	guanine37 in tRNAGlnG36A	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.36	-	guanine37 in tRNAGlnG36C	pH 8.0, temperature not specified in the publication	Haemophilus influenzae

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
8	-	assay at	Haemophilus influenzae

Cofactor

Cofactor	Comment	Organism	Structure
S-adenosyl-L-methionine	dependent on	Haemophilus influenzae
S-adenosyl-L-methionine	dependent on	Thermotoga maritima

General Information

General Information	Comment	Organism
evolution	the deep trefoil knot architecture is unique to the SpoU and tRNA methyltransferase D (TrmD) (SPOUT) family of methyltransferases (MTases) in all three domains of life	Haemophilus influenzae
evolution	the deep trefoil knot architecture is unique to the SpoU and tRNA methyltransferase D (TrmD) (SPOUT) family of methyltransferases (MTases) in all three domains of life	Thermotoga maritima
physiological function	the m1G37-modified tRNA functions properly to prevent +1 frameshift errors on the ribosome	Haemophilus influenzae
physiological function	the m1G37-modified tRNA functions properly to prevent +1 frameshift errors on the ribosome	Thermotoga maritima

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism
0.000078	-	guanine37 in tRNAGlnCUG	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.022	-	guanine37 in tRNAGlnCUG	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
0.07	-	guanine37 in tRNAGlnCUG	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
2	-	guanine37 in tRNAGlnG36C	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
15	-	guanine37 in tRNAGlnG36U	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
29	-	guanine37 in tRNAArg	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
40	-	guanine37 in tRNALeu	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
130	-	guanine37 in tRNAGlnG36A	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
130	-	guanine37 in tRNAPro	pH 8.0, temperature not specified in the publication	Haemophilus influenzae
280	-	guanine37 in tRNAGlnCUG	pH 8.0, temperature not specified in the publication	Haemophilus influenzae