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2.1.1.228: tRNA (guanine37-N1)-methyltransferase

This is an abbreviated version!
For detailed information about tRNA (guanine37-N1)-methyltransferase, go to the full flat file.

Word Map on EC 2.1.1.228

Reaction

S-adenosyl-L-methionine
+
guanine37 in tRNA
=
S-adenosyl-L-homocysteine
 +
N1-methylguanine37 in tRNA

Synonyms

At3g56120, aTrm5a methyltransferase, aTrm5a/Taw22-like enzyme, AtTrm5a, bacterial tRNA (guanine37-N1)-methyltransferase, bacterial tRNA-(N1G37) methyltransferase, EC 2.1.1.31, EcTrmD, HiTrmD, HsTrm5, m1G37 tRNA methyltransferase, m1G37-forming tRNA methyltransferase, Mj-Trm5, MJ0883, MjTrm5, MjTrm5b, mono-functional methyltransferase, More, MtbTrmD, NEQ228, PA14_15990, PAB2272, PAB_RS03940, PaTrm5a, PaTrm5b, PaTrmD, SaTrmD, Ta0997, TAW22, transfer RNA (m1G37) methyltransferase, Trm1, TRM5, Trm5a, Trm5a/Taw22-like enzyme, trm5b, Trm5p, TrmD, TRMT5, tRNA (guanine(37)-N1)-methyltransferase 1, tRNA (guanine37-N1)-methyltransferase, tRNA (guanosine-1) methyltransferase, tRNA (m1G37) methyltransferase, tRNA (m1G37)-methyltransferase, tRNA m1G37 methyltransferase, tRNA methyltransferase, tRNA methyltransferase 5, tRNA methyltransferase D, tRNA(m(1)G37)methyltransferase, tRNA(m1G37) methyltransferase, tRNA(m1G37) MTase, tRNA(m1G37)methyltransferase, tRNA-(N1G37) methyltransferase, tRNAPhe:imG2 methyltransferase

ECTree

     2 Transferases
         2.1 Transferring one-carbon groups
             2.1.1 Methyltransferases
                2.1.1.228 tRNA (guanine37-N1)-methyltransferase

Crystallization

Crystallization on EC 2.1.1.228 - tRNA (guanine37-N1)-methyltransferase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure at 2.6 A resolution
crystal structure of TrmD complexed with S-adenosyl homocysteine, determined at 2.5 A resolution
crystal structures of TrmD from Haemophilus influenzae, as binary complexes with either S-adenosyl-L-methionine or S-adenosyl-L-homocysteine, as a ternary complex with S-adenosyl-L-homocysteine and phosphate, and as an apo form
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
-
TrmD from Haemophilus influenzae with both N- and C-terminal tags is crystallized at 24°C using sodium acetate as a precipitant. Native X-ray diffraction data are collected to 1.85 A resolution. The crystals are rhombohedral, belonging to the space group R32, with unit-cell parameters a = b = 98.05, c = 176.79 A, alpha = beta = 90°, gamma = 120°
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TrmD-tRNA-sinefungin complex, crystal structure determination and analysis. In this complex structure, one TrmD homodimer is complexed with one tRNA molecule, and each TrmD monomer binds a sinefungin molecule. This binding mode is consistent with the previously reported biochemical analysis. When the substrate tRNA interacts with the catalytic pocket of subunit A, the NTDs of subunits A and B, and the neighboring CTD of subunit B, contact the tRNA. The interdomain linker of subunit B forms a helix upon tRNA binding, and participates in the interaction with the substrate tRNA
analysis of enzyme complex structures of Trm5b (MjTrm5b, PDB IDs 2YX1 and 3AY0) from Methanococcus jannaschii
analysis of the crystal structure of the Trm5-tRNA-AdoMet ternary complex
crystal structure of Trm5 in complex with the methyl donor analogue sinefungin at 2.2 A resolution, vapor diffusion method at 20°C
analysis of the crystal structure of apo-enzyme, of enzyme with bound ligand S-adenosyl-L-homocysteine (PDB IDs 5ZHI and 5ZHJ, respectively), and of enzyme with bound inhibitors N-(4-((octylamino)methyl)benzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide, N-([4-[(4-aminopiperidin-1-yl)methyl]phenyl]methyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide , and N-(4-((cyclohexyl(ethyl)amino)methyl)benzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide, PDB IDs 6JOF, 5ZHK, and 5ZHL, respectively, at resolutions of 1.75-2.76 A. Sitting drop vapor diffusion method, mixing of 0.002 ml of protein solution with 0.001 ml of precipitant solution containing 100 mM Bis-Tris propane, pH 6.5, 20% w/v PEG3350, and 0.1 M ammonium acetate, soaking of crystals with 1-5 mM inhibitor or 5 mM SAH in their respective precipitating solution supplemented with 20% v/v glycerol, X-ray diffraction structure determination and analysis
-
purified recombinant detagged enzyme TrmD as apoenzyme and in complex with S-adenosyl-L-methionine, sitting drop vapour diffusion method, for the apo-TrmD crystals, 0.001 ml of 20 mg/ml protein in storage buffer containing 25 mM HEPES, pH 7.5, 500 mM NaCl, and 5% glycerol are mixed with 0.001 ml of reservoir solution containing 0.08 mM sodium cacodylate pH 6.5-7.0, 1-2 M and ammonium sulfate, and equilibrated against 0.25 ml of reservoir solution, the apo crystals formed are allowed to soak in a 0.004 ml drop containing reservoir solution and 10 mM ligand (in DMSO) and equilibrated against 0.7 ml of the corresponding reservoir solution overnight at 19°C in hanging drop vapor diffusion plates, X-ray diffraction structure determination and analysis at 1.67 A resolution, molecular replacement using the solved Mab TrmD apo structure (PDB code 6NVR) as a search model
-
analysis of the crystal structure of enzyme with bound inhibitors N-([4-[(4-aminopiperidin-1-yl)methyl]phenyl]methyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide, N-(4-((diethylamino)methyl)benzyl)-4-oxo-3,4-dihydrothieno-[2,3-d]pyrimidine-5-carboxamide, and N-(4-((octylamino)methyl)benzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide, PDB IDs 6JOE, 5ZHM, and 5ZHN, respectively. Hanging drop vapor diffusion method, mixing of equal volumes of 20 mg/m protein and precipitant solution containing 0.1 M Tris-HCl, pH 8.6-8.8, 20% v/v MPD, 20% w/v PEG 1000, and 5% w/v PEG200, and incubation at 20°C, soaking of crystals with 1-5 mM inhibitor in the precipitating solution supplemented with 20% v/v glycerol at 20°C for at least 4 h, X-ray diffraction structure determination and analysis
-
purified recombinant PaTrmD in complex with SAM, mixing equal volumes of protein and precipitant solution containing 0.1 M Tris-HCl, pH 8.4, 12.5% v/v MPD, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350 and 5% w/v PEG 200, the enzyme inhibitor complex PaTrmD-sinefungin crystals are obtained by soaking the PaTrmD-SAM crystals in the precipitating solution supplemented with 2 mM sinefungin at 20°C for 2 h, for the complex with SFG and Mn2+, one crystal of PaTrmD-SAM is soaked in the precipitating solution supplemented with 10% (v/v) glycerol, 2 mM sinefungin and 5 mM MnCl2 at 20°C for 24 h, X-ray diffraction structure determination and analysis at 2.16 A resolution
purified recombinant apo-PaTrm5a and PaTrm5a in complex with tRNAPhe, with SAM, and as PaTrm5a-tRNAPhe (imG-14)-SAH ternary complex, sitting drop vapor diffusion method, 6 mg/ml recombinant His6-tagged enzyme protein is mixed with tRNAPhe at a molar ratio of 1:0.4 in a buffer containing 20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM DTT, and 1.5 mM SAH or SAM, and equilibration against a reservoir solution containing 45% 2-methyl-2,4-pentanediol, 100 mM MES, pH 6.5, and 200 mM NH4OAc, 1 week, X-ray diffraction structure determination and analysis at 2.6-3.2 A resolution, molecular replacement using complex structure of the MjTrm5b-tRNACys-SAM complex (PDB ID 2ZZN) as the search model, modelling
purified recombinant enzyme full-length PaTrm5b in the apo-form, sitting drop vapor diffusion method, 25°C, the sample and the well solution are mixed at a 1:1 volume ratio. The condition contains 10% w/v PEG 3350, 100 mM HEPES, pH 7.5, 100 mM Ca(OAc)2, and 100 mM KCl, iterative seeding is employed to obtain diffraction-quality crystals, X-ray diffraction structure determination and analysis at 3.3 A resolution, molecular replacement using the coordinates of the PaTrm5a structure (PDB 5HJM) as the search model, modeling. The removal or relocation of the His6-tag to the C-terminus fails to generate crystals, as does the removal of the D1 domain, although both constructs show comparable stability to the N-terminally His6-tagged PaTrm5b protein. Furthermore, the addition of SAM, SAH or other SAM analogues to the crystallization sample either generates tiny crystals unsuitable for data collection or no crystals altogether
purified recombinant PaTrm5a in apo form and in complex with various SAM analogues, mixing PaTrm5a with 1.5 mM SAH or SAM at a protein: ligand molar ratio of 1:3, sitting drop vapor diffusion method, mixing 20 mg/ml protein solution in a 1:1 ratio with well solution containing w/v PEG 3350, 100 mM HEPES, pH 7.5, 100 mM Ca(OAc)2 and 100 mM KCl, method optimmization, 25°C, X-ray diffraction structure determination and analysis at 1.76-2.20 A resolution
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
-