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 Maximum [mM] | Substrate | Comment | 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 | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
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 | UniProt | Comment | Textmining |
---|---|---|---|
Haemophilus influenzae | - |
gene trmD | - |
Haemophilus influenzae DSM 11121 | - |
gene trmD | - |
Thermotoga maritima | - |
gene trmD | - |
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 | |
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 | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
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 | 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 | Comment | Organism |
---|---|---|
TrmD | - |
Haemophilus influenzae |
TrmD | - |
Thermotoga maritima |
Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | 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 Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
8 | - |
assay at | Haemophilus influenzae |
Cofactor | Comment | Organism | Structure |
---|---|---|---|
S-adenosyl-L-methionine | dependent on | Haemophilus influenzae | |
S-adenosyl-L-methionine | dependent on | Thermotoga maritima |
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 Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | 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 |