BRENDA - Enzyme Database
show all sequences of 2.1.1.228

Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD

Ito, T.; Masuda, I.; Yoshida, K.; Goto-Ito, S.; Sekine, S.; Suh, S.W.; Hou, Y.M.; Yokoyama, S.; Proc. Natl. Acad. Sci. USA 112, E4197-E4205 (2015) View publication on PubMedView publication on EuropePMC

Data extracted from this reference:

Crystallization (Commentary)
Crystallization (Commentary)
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
Commentary
Organism
Structure
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
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
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
Commentary
Textmining
Haemophilus influenzae
-
gene trmD
-
Haemophilus influenzae DSM 11121
-
gene trmD
-
Thermotoga maritima
-
gene trmD
-
Reaction
Reaction
Commentary
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
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
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
S-adenosyl-L-methionine + guanine37 in tRNA
-
737174
Haemophilus influenzae
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
-
737174
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
737174
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
737174
Thermotoga maritima
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
-
737174
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
737174
Haemophilus influenzae DSM 11121
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAArg
tRNA substrate from Haemophilus influenzae
737174
Haemophilus influenzae
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAArg
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAArg
tRNA substrate from Haemophilus influenzae
737174
Haemophilus influenzae DSM 11121
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAArg
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAGlnCUG
-
737174
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
737174
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
737174
Haemophilus influenzae DSM 11121
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAGlnCUG
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAGlnG36A
tRNA substrate from Thermotoga maritima
737174
Haemophilus influenzae
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAGlnG36A
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAGlnG36C
tRNA substrate from Thermotoga maritima
737174
Haemophilus influenzae
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAGlnG36C
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAGlnG36U
tRNA substrate from Thermotoga maritima
737174
Haemophilus influenzae
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAGlnG36U
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNALeu
tRNA substrate from Haemophilus influenzae
737174
Haemophilus influenzae
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNALeu
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNALeu
tRNA substrate from Haemophilus influenzae
737174
Haemophilus influenzae DSM 11121
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNALeu
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAPro
tRNA substrate from Haemophilus influenzae
737174
Haemophilus influenzae
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAPro
-
-
-
?
Subunits
Subunits
Commentary
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
Commentary
Organism
TrmD
-
Haemophilus influenzae
TrmD
-
Thermotoga maritima
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
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
Commentary
Organism
8
-
assay at
Haemophilus influenzae
Cofactor
Cofactor
Commentary
Organism
Structure
S-adenosyl-L-methionine
dependent on
Haemophilus influenzae
S-adenosyl-L-methionine
dependent on
Thermotoga maritima
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
S-adenosyl-L-methionine
dependent on
Haemophilus influenzae
S-adenosyl-L-methionine
dependent on
Thermotoga maritima
Crystallization (Commentary) (protein specific)
Crystallization
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] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
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) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
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
-
-
?
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
S-adenosyl-L-methionine + guanine37 in tRNA
-
737174
Haemophilus influenzae
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
-
737174
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
737174
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
737174
Thermotoga maritima
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNA
-
737174
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
737174
Haemophilus influenzae DSM 11121
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAArg
tRNA substrate from Haemophilus influenzae
737174
Haemophilus influenzae
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAArg
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAArg
tRNA substrate from Haemophilus influenzae
737174
Haemophilus influenzae DSM 11121
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAArg
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAGlnCUG
-
737174
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
737174
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
737174
Haemophilus influenzae DSM 11121
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAGlnCUG
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAGlnG36A
tRNA substrate from Thermotoga maritima
737174
Haemophilus influenzae
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAGlnG36A
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAGlnG36C
tRNA substrate from Thermotoga maritima
737174
Haemophilus influenzae
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAGlnG36C
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAGlnG36U
tRNA substrate from Thermotoga maritima
737174
Haemophilus influenzae
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAGlnG36U
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNALeu
tRNA substrate from Haemophilus influenzae
737174
Haemophilus influenzae
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNALeu
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNALeu
tRNA substrate from Haemophilus influenzae
737174
Haemophilus influenzae DSM 11121
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNALeu
-
-
-
?
S-adenosyl-L-methionine + guanine37 in tRNAPro
tRNA substrate from Haemophilus influenzae
737174
Haemophilus influenzae
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAPro
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
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
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
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 (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Haemophilus influenzae
General Information
General Information
Commentary
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
General Information (protein specific)
General Information
Commentary
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
Commentary
Organism
Structure
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
KCat/KM [mM/s] (protein specific)
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
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
Other publictions for EC 2.1.1.228
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Synonyms
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
755697
Zhong
Targeting the bacterial epitr ...
Pseudomonas aeruginosa, Pseudomonas aeruginosa UCBPP-PA14
ACS Infect. Dis.
5
326-335
2019
-
1
1
-
-
-
63
2
-
-
-
2
-
8
-
-
-
-
-
-
-
-
6
-
3
-
-
1
2
-
-
-
1
-
-
63
-
1
1
1
-
-
-
63
63
-
2
-
-
-
2
-
-
-
-
-
-
-
-
6
-
-
-
1
2
-
-
-
-
-
1
1
-
2
2
756152
Li
Backbone resonance assignment ...
Pseudomonas aeruginosa, Pseudomonas aeruginosa UCBPP-PA14
Biomol. NMR Assign.
13
327-332
2019
-
1
1
-
-
-
1
-
-
-
-
2
-
7
-
-
1
-
-
1
-
-
2
2
2
-
-
-
-
1
-
-
1
-
-
-
-
1
1
1
-
-
-
-
1
-
-
-
-
-
2
-
-
-
1
-
1
-
-
2
2
-
-
-
-
1
-
-
-
-
2
2
-
-
-
756153
Li
Backbone resonance assignment ...
Pseudomonas aeruginosa, Pseudomonas aeruginosa UCBPP-PA14
Biomol. NMR Assign.
13
49-53
2019
-
-
1
-
-
-
2
-
-
-
-
2
-
6
-
-
1
-
-
-
-
-
2
-
2
-
-
1
-
-
-
-
1
-
-
-
-
-
1
1
-
-
-
-
2
-
-
-
-
-
2
-
-
-
1
-
-
-
-
2
-
-
-
1
-
-
-
-
-
-
1
1
-
-
-
756774
Hou
Codon-specific translation by ...
Escherichia coli, Salmonella enterica subsp. enterica serovar Typhimurium, Saccharomyces cerevisiae, Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412, Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720, Saccharomyces cerevisiae ATCC 204508
Front. Genet.
10
713
2019
-
-
-
-
1
-
-
-
-
2
-
7
-
8
-
-
-
-
-
-
-
-
7
-
4
-
-
-
-
-
-
-
3
-
-
-
-
-
-
3
-
1
-
-
-
-
-
-
2
-
7
-
-
-
-
-
-
-
-
7
-
-
-
-
-
-
-
-
-
1
8
8
1
-
-
757408
Whitehouse
Development of inhibitors aga ...
Mycobacteroides abscessus
J. Med. Chem.
62
7210-7232
2019
-
1
1
1
-
-
50
-
-
-
-
1
-
6
-
-
1
-
-
-
-
-
1
1
2
-
-
-
-
-
-
-
1
-
-
-
-
1
1
1
1
-
-
-
50
-
-
-
-
-
1
-
-
-
1
-
-
-
-
1
1
-
-
-
-
-
-
-
-
-
2
2
-
-
-
757409
Zhong
Thienopyrimidinone derivative ...
Staphylococcus aureus, Mycobacterium tuberculosis, Pseudomonas aeruginosa
J. Med. Chem.
62
7788-7805
2019
-
-
3
2
-
3
42
3
-
2
-
3
-
5
-
-
-
-
-
-
-
-
3
-
12
1
-
-
-
1
-
-
3
-
-
26
-
-
3
3
2
-
3
26
42
-
3
-
2
-
3
-
-
-
-
-
-
-
-
3
-
1
-
-
-
1
-
-
-
-
3
3
-
-
-
757863
Jin
AtTrm5a catalyses 1-methylgua ...
Arabidopsis thaliana
Nucleic Acids Res.
47
883-898
2019
-
-
1
-
1
-
-
-
1
1
-
2
-
8
-
-
1
-
-
2
-
-
2
-
3
1
-
-
-
1
-
-
1
-
-
-
-
-
1
1
-
1
-
-
-
-
-
1
1
-
2
-
-
-
1
-
2
-
-
2
-
1
-
-
-
1
-
-
-
-
2
2
-
-
-
758329
Jaroensuk
Crystal structure and catalyt ...
Pseudomonas aeruginosa, Pseudomonas aeruginosa UCBPP-PA14
RNA
25
1481-1496
2019
-
1
1
1
1
-
1
3
-
2
-
2
-
10
-
-
1
-
-
-
-
-
14
2
5
1
-
-
2
1
-
-
1
3
-
-
-
1
1
1
1
1
-
-
1
3
3
-
2
-
2
-
-
-
1
-
-
-
-
14
2
1
-
-
2
1
-
-
-
-
2
2
-
2
2
757201
Zhou
A hypertension-associated mit ...
Methanocaldococcus jannaschii, Methanocaldococcus jannaschii NBRC 100440, Methanocaldococcus jannaschii DSM 2661, Methanocaldococcus jannaschii ATCC 43067, Methanocaldococcus jannaschii JAL-1, Methanocaldococcus jannaschii JCM 10045
J. Biol. Chem.
293
1425-1438
2018
-
-
-
-
1
-
-
-
-
-
-
6
-
17
-
-
-
-
-
-
-
-
12
-
5
-
-
-
-
-
-
-
1
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
6
-
-
-
-
-
-
-
-
12
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
755960
Wu
The crystal structure of the ...
Pyrococcus abyssi
Biochem. Biophys. Res. Commun.
493
240-245
2017
-
-
1
1
1
-
-
-
-
-
-
1
-
9
-
-
1
-
-
-
-
-
2
1
4
1
-
-
-
1
-
-
1
-
-
-
-
-
1
1
1
1
-
-
-
-
-
-
-
-
1
-
-
-
1
-
-
-
-
2
1
1
-
-
-
1
-
-
-
-
4
4
-
-
-
756161
Goto-Ito
Trm5 and TrmD two enzymes fr ...
Escherichia coli, Haemophilus influenzae, Methanocaldococcus jannaschii, Pyrococcus abyssi, Pyrococcus abyssi Orsay, Methanocaldococcus jannaschii NBRC 100440, Haemophilus influenzae RD, Methanocaldococcus jannaschii DSM 2661, Methanocaldococcus jannaschii ATCC 43067, Methanocaldococcus jannaschii JAL-1, Haemophilus influenzae DSM 11121, Haemophilus influenzae KW20, Haemophilus influenzae ATCC 51907, Methanocaldococcus jannaschii JCM 10045
Biomolecules
7
32
2017
-
-
-
1
-
-
-
4
-
-
-
16
-
36
-
-
-
-
-
-
-
-
30
4
10
-
-
-
-
-
-
-
4
-
-
-
-
-
-
4
1
-
-
-
-
-
4
-
-
-
16
-
-
-
-
-
-
-
-
30
4
-
-
-
-
-
-
-
-
-
14
14
-
-
-
756163
Hori
Transfer RNA methyltransferas ...
Haemophilus influenzae, Aquifex aeolicus, Escherichia coli
Biomolecules
7
E23
2017
-
-
-
-
-
-
-
-
-
-
-
3
-
3
-
-
-
-
-
-
-
-
6
3
3
-
-
-
-
-
-
-
3
-
-
-
-
-
-
3
-
-
-
-
-
-
-
-
-
-
3
-
-
-
-
-
-
-
-
6
3
-
-
-
-
-
-
-
-
-
7
7
-
-
-
756631
Hou
TrmD A methyl transferase fo ...
Haemophilus influenzae, Aquifex aeolicus, Escherichia coli, Salmonella enterica subsp. enterica serovar Typhimurium, Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412, Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720
Enzymes
41
89-115
2017
-
4
4
-
-
-
-
-
-
16
-
12
-
8
-
-
-
-
-
-
-
-
12
8
6
-
-
-
-
-
-
-
4
-
-
-
-
4
4
4
-
-
-
-
-
-
-
-
16
-
12
-
-
-
-
-
-
-
-
12
8
-
-
-
-
-
-
-
-
-
16
16
-
-
-
758348
Wang
Structural insight into the m ...
Methanocaldococcus jannaschii, Pyrococcus abyssi, Methanocaldococcus jannaschii DSM 2661
Sci. Adv.
3
e1700195
2017
-
-
1
2
7
-
-
-
-
2
-
4
-
6
-
-
1
-
-
-
-
-
7
1
6
2
-
-
-
2
-
-
2
-
-
-
-
-
1
2
2
7
-
-
-
-
-
-
2
-
4
-
-
-
1
-
-
-
-
7
1
2
-
-
-
2
-
-
-
-
4
4
-
-
-
757790
Christian
Methyl transfer by substrate ...
Haemophilus influenzae
Nat. Struct. Mol. Biol.
23
941-948
2016
-
1
-
-
-
-
1
-
-
-
-
2
-
1
-
-
-
-
-
-
-
-
2
1
2
-
-
-
-
-
-
-
1
-
-
-
-
1
-
1
-
-
-
-
1
-
-
-
-
-
2
-
-
-
-
-
-
-
-
2
1
-
-
-
-
-
-
-
-
-
4
4
-
-
-
758324
Urbonavicius
Evolution of tRNAPhe imG2 met ...
Nanoarchaeum equitans, Pyrococcus abyssi, Pyrococcus abyssi Orsay
RNA
22
1871-1883
2016
-
-
2
-
7
-
-
-
-
2
-
11
-
4
-
-
2
-
-
-
-
-
19
-
14
2
-
-
-
2
-
-
2
-
-
-
-
-
2
2
-
7
-
-
-
-
-
-
2
-
11
-
-
-
2
-
-
-
-
19
-
2
-
-
-
2
-
-
-
-
8
8
-
-
-
758376
Wang
Crystal structures of the bif ...
Pyrococcus abyssi
Sci. Rep.
6
33553
2016
-
-
1
1
2
-
-
-
-
1
-
2
-
9
-
-
1
-
-
-
-
-
3
2
5
-
-
-
-
-
-
-
1
-
-
-
-
-
1
1
1
2
-
-
-
-
-
-
1
-
2
-
-
-
1
-
-
-
-
3
2
-
-
-
-
-
-
-
-
-
4
4
-
-
-
735421
Powell
TRMT5 mutations cause a defect ...
Homo sapiens
Am. J. Hum. Genet.
97
319-328
2015
-
-
1
-
3
-
-
-
1
-
-
1
-
7
-
-
-
-
-
-
-
-
1
1
2
-
-
-
-
-
-
-
1
-
-
-
-
-
1
1
-
3
-
-
-
-
-
1
-
-
1
-
-
-
-
-
-
-
-
1
1
-
-
-
-
-
-
-
-
-
4
4
-
-
-
737174
Ito
Structural basis for methyl-do ...
Haemophilus influenzae, Thermotoga maritima, Haemophilus influenzae DSM 11121
Proc. Natl. Acad. Sci. USA
112
E4197-E4205
2015
-
-
-
2
-
-
-
12
-
-
-
3
-
4
-
-
-
2
-
-
-
-
17
2
2
-
-
-
10
1
-
-
2
-
-
-
-
-
-
2
2
-
-
-
-
-
12
-
-
-
3
-
-
-
-
-
-
-
-
17
2
-
-
-
10
1
-
-
-
-
4
4
-
10
10
757582
Hou
Kinetic analysis of tRNA meth ...
Escherichia coli, Haemophilus influenzae, Homo sapiens, Methanocaldococcus jannaschii, Methanocaldococcus jannaschii NBRC 100440, Haemophilus influenzae RD, Methanocaldococcus jannaschii DSM 2661, Methanocaldococcus jannaschii ATCC 43067, Methanocaldococcus jannaschii JAL-1, Haemophilus influenzae DSM 11121, Haemophilus influenzae KW20, Haemophilus influenzae ATCC 51907, Methanocaldococcus jannaschii JCM 10045
Methods Enzymol.
560
91-116
2015
-
-
-
-
-
-
-
4
-
4
-
13
-
28
-
-
-
-
-
-
-
-
26
-
13
4
-
-
-
4
-
-
4
-
-
-
-
-
-
4
-
-
-
-
-
-
4
-
4
-
13
-
-
-
-
-
-
-
-
26
-
4
-
-
-
4
-
-
-
-
12
12
-
-
-
729858
Kawamura
Transfer RNA methyltransferase ...
Thermoplasma acidophilum, Thermoplasma acidophilum HO-62
Int. J. Mol. Sci.
16
91-113
2014
-
-
1
-
-
-
-
-
-
-
-
-
-
9
-
-
1
-
-
-
-
-
1
-
2
1
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
1
-
1
-
-
-
1
-
-
-
-
-
-
-
-
-
735927
Sakaguchi
A divalent metal ion-dependent ...
Escherichia coli
Chem. Biol.
21
1351-1360
2014
-
1
-
-
-
-
-
1
-
4
-
1
-
1
-
-
-
1
-
-
-
-
2
1
1
-
-
-
-
-
-
-
1
-
-
-
-
1
-
1
-
-
-
-
-
-
1
-
4
-
1
-
-
-
-
-
-
-
-
2
1
-
-
-
-
-
-
-
-
-
2
2
-
-
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The temperature sensitivity of ...
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6
1
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737226
Christian
Conservation of structure and ...
Homo sapiens
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19
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2013
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9
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1
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1
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1
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2
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1
1
737228
Paris
The T. brucei TRM5 methyltrans ...
Trypanosoma brucei brucei, Trametes pubescens 927 / 4 GUTat10.1 / TREU927
RNA
19
649-658
2013
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12
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2
2
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721035
Sakaguchi
Recognition of guanosine by di ...
Escherichia coli, Methanocaldococcus jannaschii
RNA
18
1687-1701
2012
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-
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2
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2
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2
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2
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10
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10
-
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2
2
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721029
Lahoud
Differentiating analogous tRNA ...
Escherichia coli, Methanocaldococcus jannaschii
RNA
17
1236-1246
2011
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-
-
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24
2
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2
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2
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2
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24
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24
24
2
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2
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2
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Christian
Control of catalytic cycle by ...
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204-217
2010
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6
2
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3
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721026
Christian
Mechanism of N-methylation by ...
Methanocaldococcus jannaschii
RNA
16
2484-2492
2010
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1
18
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1
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1
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1
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1
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1
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3
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2
1
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1
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1
1
18
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1
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1
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1
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3
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1
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1
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701123
Goto-Ito
Crystal structure of archaeal ...
Methanocaldococcus jannaschii
Proteins
72
1274-1289
2008
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1
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11
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1
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1
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1
1
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1
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1
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1
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1
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1
-
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1
1
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-
-
-
-
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1
1
712103
Toyooka
Stabilization of tRNA (mG37) m ...
Aquifex aeolicus
Genes Cells
13
807-816
2008
-
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-
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1
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-
-
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1
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1
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1
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687609
Lee
Yeast mitochondrial initiator ...
Saccharomyces cerevisiae
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282
27744-27753
2007
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1
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1
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2
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1
1
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1
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1
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2
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1
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2
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1
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1
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712739
Christian
Distinct determinants of tRNA ...
Escherichia coli, Methanocaldococcus jannaschii
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2007
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2
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5
2
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5
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5
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2
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5
2
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2
2
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5
5
673850
Takeda
The substrate specificity of t ...
Aquifex aeolicus
Genes Cells
11
1353-1365
2006
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1
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13
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1
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6
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1
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15
-
3
1
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1
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1
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13
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1
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1
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15
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1
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1
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-
711197
Christian
Catalysis by the second class ...
Methanocaldococcus jannaschii
Biochemistry
45
7463-7473
2006
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9
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11
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1
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1
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1
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2
1
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11
1
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9
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11
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1
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1
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1
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11
1
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1
1
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11
11
661154
Brule
Isolation and characterization ...
Escherichia coli, Homo sapiens
Biochemistry
43
9243-9255
2004
1
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2
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13
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3
2
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9
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20
2
4
2
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4
2
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1
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2
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5
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13
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3
2
2
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2
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20
2
2
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4
2
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662010
O'Dwyer
Characterization of Streptococ ...
Streptococcus pneumoniae
J. Bacteriol.
186
2346-2354
2004
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1
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1
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1
1
1
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2
2
1
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1
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2
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4
3
1
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1
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3
1
1
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2
2
1
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2
2
662622
Christian
Distinct origins of tRNA(m1G37 ...
Methanocaldococcus jannaschii
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707-719
2004
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1
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1
1
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1
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661585
Ahn
Crystal structure of tRNA(m1G3 ...
Haemophilus influenzae
EMBO J.
22
2593-2603
2003
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1
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1
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1
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712737
Elkins
Insights into catalysis by a k ...
Escherichia coli
J. Mol. Biol.
333
931-949
2003
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1
1
44
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1
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1
44
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2
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1
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713482
Liu
Crystal structure of tRNA (m1G ...
Aquifex aeolicus
Proteins
53
326-328
2003
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1
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1
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1
1
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710708
Kim
Crystallization and preliminar ...
Haemophilus influenzae
Acta Crystallogr. Sect. D
59
183-184
2002
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1
1
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