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show all sequences of 2.1.1.256

Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life

Fislage, M.; Roovers, M.; Tuszynska, I.; Bujnicki, J.M.; Droogmans, L.; Versees, W.; Nucleic Acids Res. 40, 5149-5161 (2012)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
expression of the N-terminally His-tagged emzyme in in Escherichia coli strain Rosetta (DE3)
Pyrococcus furiosus
expression of the N-terminally His-tagged enzyme in in Escherichia coli strain BL21 (DE3)
Thermus thermophilus
Crystallization (Commentary)
Crystallization
Organism
purified recombinant detagged enzyme in complex with S-adenosyl-L-methionine or reaction product S-adenosyl-homocysteine, and inhibitor sinefungin, hanging drop vapor diffusion, protein in 50 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 500 mM NaCl, 280 mM imidazole, and 1 mM DTT, mixing in a 1:1 ratio with crystallization solution containing 100 mM Tris-acetate, pH 8.0, 32% PEG 4000, and 15% glycerol, for the phasing, selenomethionine-derivatized PfTrm14 is crystallized in a crystallization solution containing 100 mM Tris-acetate, pH 8.0, 32% PEG 4000, 15% glycerol, after streak seeding from a native PfTrm14 crystal, crystal soaking in mother liquor containing 1 mM ligand, X-ray diffraction structure determination and analysis at 1.95-2.4 A resolution
Pyrococcus furiosus
purified recombinant His-tagged enzyme in complex with S-adenosyl-L-methionine or reaction product S-adenosyl-homocysteine, and inhibitor sinefungin, hanging drop vapor diffusion, protein in 50 mM Tris-HCl, pH 8.0, 250 mM NaCl, and 350 mM imidazole, mixing in a 1:1 ratio with crystallization solution 100 mM citrate/phosphate, pH 3.5, 15% PEG 6000, 200 mM NaCl, and 100 mM sodium citrate, crystal soaking in mother liquor containing 1 mM ligand, X-ray diffraction structure determination and analysis at 2.16 A resolution, solved in the apo state by molecular replacement to a resolution of 2.05 A
Thermus thermophilus
Inhibitors
Inhibitors
Commentary
Organism
Structure
sinefungin
-
Pyrococcus furiosus
sinefungin
-
Thermus thermophilus
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Mg2+
required
Pyrococcus furiosus
Mg2+
required
Thermus thermophilus
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
S-adenosyl-L-methionine + guanine6 in tRNA
Thermus thermophilus
the enzyme specifically modifies tRNAPhe at guanosine 6 in the tRNA acceptor stem
S-adenosyl-L-homocysteine + N2-methylguanine6 in tRNA
-
-
?
S-adenosyl-L-methionine + guanine6 in tRNA
Pyrococcus furiosus
the enzyme specifically modifies tRNAPhe at guanosine 6 in the tRNA acceptor stem
S-adenosyl-L-homocysteine + N2-methylguanine6 in tRNA
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Pyrococcus furiosus
Q8U248
gene PF1002
-
Thermus thermophilus
Q72IH5
gene TTC1157
-
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
additional information
active site structure with bound ligands, S-adenosyl-L-methionine, S-adenosyl-L-homocysteine, and sinefungin, overview
720602
Pyrococcus furiosus
?
-
-
-
-
additional information
docking model of TrmN in complex with tRNAPhe of Thermus thermophilus
720602
Thermus thermophilus
?
-
-
-
-
S-adenosyl-L-methionine + guanine6 in tRNA
the enzyme specifically modifies tRNAPhe at guanosine 6 in the tRNA acceptor stem
720602
Thermus thermophilus
S-adenosyl-L-homocysteine + N2-methylguanine6 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine6 in tRNA
the enzyme specifically modifies tRNAPhe at guanosine 6 in the tRNA acceptor stem
720602
Pyrococcus furiosus
S-adenosyl-L-homocysteine + N2-methylguanine6 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine6 in tRNA
the enzyme specifically modifies tRNAPhe at guanosine 6 in the tRNA acceptor stem. Contribution of the THUMP domain in tRNA recognition and catalysis, substrate binding and ligand-induced conformational changes in the RFM domain
720602
Pyrococcus furiosus
S-adenosyl-L-homocysteine + N2-methylguanine6 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine6 in tRNA
the enzyme specifically modifies tRNAPhe at guanosine 6 in the tRNA acceptor stem. Contribution of the THUMP domain in tRNA recognition and catalysis, substrate binding and ligand-induced conformational changes in the RFM domain, overview
720602
Thermus thermophilus
S-adenosyl-L-homocysteine + N2-methylguanine6 in tRNA
-
-
-
?
Subunits
Subunits
Commentary
Organism
More
the enzyme consists of an N-terminal THUMP domain fused to a catalytic Rossmann-fold MTase domain, with the main tRNA binding surface in a groove between the THUMP domain and the MTase domain, secondary sequence comparison, overview
Pyrococcus furiosus
More
the enzyme consists of an N-terminal THUMP domain fused to a catalytic Rossmann-fold MTase domain, with the main tRNA binding surface in a groove between the THUMP domain and the MTase domain, secondary sequence comparison, overview
Thermus thermophilus
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
60
-
assay at
Thermus thermophilus
70
-
assay at
Pyrococcus furiosus
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Pyrococcus furiosus
8
-
assay at
Thermus thermophilus
Cloned(Commentary) (protein specific)
Commentary
Organism
expression of the N-terminally His-tagged emzyme in in Escherichia coli strain Rosetta (DE3)
Pyrococcus furiosus
expression of the N-terminally His-tagged enzyme in in Escherichia coli strain BL21 (DE3)
Thermus thermophilus
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant detagged enzyme in complex with S-adenosyl-L-methionine or reaction product S-adenosyl-homocysteine, and inhibitor sinefungin, hanging drop vapor diffusion, protein in 50 mM Tris-HCl, pH 8.0, 10 mM MgCl2, 500 mM NaCl, 280 mM imidazole, and 1 mM DTT, mixing in a 1:1 ratio with crystallization solution containing 100 mM Tris-acetate, pH 8.0, 32% PEG 4000, and 15% glycerol, for the phasing, selenomethionine-derivatized PfTrm14 is crystallized in a crystallization solution containing 100 mM Tris-acetate, pH 8.0, 32% PEG 4000, 15% glycerol, after streak seeding from a native PfTrm14 crystal, crystal soaking in mother liquor containing 1 mM ligand, X-ray diffraction structure determination and analysis at 1.95-2.4 A resolution
Pyrococcus furiosus
purified recombinant His-tagged enzyme in complex with S-adenosyl-L-methionine or reaction product S-adenosyl-homocysteine, and inhibitor sinefungin, hanging drop vapor diffusion, protein in 50 mM Tris-HCl, pH 8.0, 250 mM NaCl, and 350 mM imidazole, mixing in a 1:1 ratio with crystallization solution 100 mM citrate/phosphate, pH 3.5, 15% PEG 6000, 200 mM NaCl, and 100 mM sodium citrate, crystal soaking in mother liquor containing 1 mM ligand, X-ray diffraction structure determination and analysis at 2.16 A resolution, solved in the apo state by molecular replacement to a resolution of 2.05 A
Thermus thermophilus
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
sinefungin
-
Pyrococcus furiosus
sinefungin
-
Thermus thermophilus
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Mg2+
required
Pyrococcus furiosus
Mg2+
required
Thermus thermophilus
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
S-adenosyl-L-methionine + guanine6 in tRNA
Thermus thermophilus
the enzyme specifically modifies tRNAPhe at guanosine 6 in the tRNA acceptor stem
S-adenosyl-L-homocysteine + N2-methylguanine6 in tRNA
-
-
?
S-adenosyl-L-methionine + guanine6 in tRNA
Pyrococcus furiosus
the enzyme specifically modifies tRNAPhe at guanosine 6 in the tRNA acceptor stem
S-adenosyl-L-homocysteine + N2-methylguanine6 in tRNA
-
-
?
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
additional information
active site structure with bound ligands, S-adenosyl-L-methionine, S-adenosyl-L-homocysteine, and sinefungin, overview
720602
Pyrococcus furiosus
?
-
-
-
-
additional information
docking model of TrmN in complex with tRNAPhe of Thermus thermophilus
720602
Thermus thermophilus
?
-
-
-
-
S-adenosyl-L-methionine + guanine6 in tRNA
the enzyme specifically modifies tRNAPhe at guanosine 6 in the tRNA acceptor stem
720602
Thermus thermophilus
S-adenosyl-L-homocysteine + N2-methylguanine6 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine6 in tRNA
the enzyme specifically modifies tRNAPhe at guanosine 6 in the tRNA acceptor stem
720602
Pyrococcus furiosus
S-adenosyl-L-homocysteine + N2-methylguanine6 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine6 in tRNA
the enzyme specifically modifies tRNAPhe at guanosine 6 in the tRNA acceptor stem. Contribution of the THUMP domain in tRNA recognition and catalysis, substrate binding and ligand-induced conformational changes in the RFM domain
720602
Pyrococcus furiosus
S-adenosyl-L-homocysteine + N2-methylguanine6 in tRNA
-
-
-
?
S-adenosyl-L-methionine + guanine6 in tRNA
the enzyme specifically modifies tRNAPhe at guanosine 6 in the tRNA acceptor stem. Contribution of the THUMP domain in tRNA recognition and catalysis, substrate binding and ligand-induced conformational changes in the RFM domain, overview
720602
Thermus thermophilus
S-adenosyl-L-homocysteine + N2-methylguanine6 in tRNA
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
More
the enzyme consists of an N-terminal THUMP domain fused to a catalytic Rossmann-fold MTase domain, with the main tRNA binding surface in a groove between the THUMP domain and the MTase domain, secondary sequence comparison, overview
Pyrococcus furiosus
More
the enzyme consists of an N-terminal THUMP domain fused to a catalytic Rossmann-fold MTase domain, with the main tRNA binding surface in a groove between the THUMP domain and the MTase domain, secondary sequence comparison, overview
Thermus thermophilus
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
60
-
assay at
Thermus thermophilus
70
-
assay at
Pyrococcus furiosus
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
8
-
assay at
Pyrococcus furiosus
8
-
assay at
Thermus thermophilus
General Information
General Information
Commentary
Organism
evolution
RNA MTases from the TrmN/Trm14 family are present in archaea, bacteria and eukaryota and all specifically modify tRNAPhe at guanosine 6 in the tRNA acceptor stem. RNA MTases can be classified into four superfamilies, overview
Pyrococcus furiosus
evolution
RNA MTases from the TrmN/Trm14 family are present in archaea, bacteria and eukaryota and all specifically modify tRNAPhe at guanosine 6 in the tRNA acceptor stem. RNA MTases can be classified into four superfamilies, overview
Thermus thermophilus
General Information (protein specific)
General Information
Commentary
Organism
evolution
RNA MTases from the TrmN/Trm14 family are present in archaea, bacteria and eukaryota and all specifically modify tRNAPhe at guanosine 6 in the tRNA acceptor stem. RNA MTases can be classified into four superfamilies, overview
Pyrococcus furiosus
evolution
RNA MTases from the TrmN/Trm14 family are present in archaea, bacteria and eukaryota and all specifically modify tRNAPhe at guanosine 6 in the tRNA acceptor stem. RNA MTases can be classified into four superfamilies, overview
Thermus thermophilus
Other publictions for EC 2.1.1.256
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
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)
720602
Fislage
Crystal structures of the tRNA ...
Pyrococcus furiosus, Thermus thermophilus
Nucleic Acids Res.
40
5149-5161
2012
-
-
2
2
-
-
2
-
-
2
-
2
-
7
-
-
-
-
-
-
-
-
6
2
2
-
-
-
2
-
-
-
-
-
-
-
-
2
-
2
-
-
-
2
-
-
-
2
-
2
-
-
-
-
-
-
-
-
6
2
2
-
-
-
2
-
-
-
-
2
2
-
-
-
746421
Roovers
The open reading frame TTC115 ...
Pyrococcus furiosus, Thermus thermophilus, Thermus thermophilus DSM 7039
RNA
18
815-824
2012
-
-
2
-
-
-
-
-
-
-
-
-
-
6
-
-
2
-
-
-
-
-
3
1
-
-
-
-
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
2
-
-
-
-
3
1
-
-
-
-
-
-
-
-
-
1
1
-
-
-
720590
Menezes
Formation of m2G6 in Methanoca ...
Methanocaldococcus jannaschii, Methanocaldococcus jannaschii JAL-1
Nucleic Acids Res.
39
7641-7655
2011
-
-
1
-
-
-
-
1
-
1
-
2
-
4
-
-
-
-
-
-
-
-
4
1
1
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
1
-
1
-
2
-
-
-
-
-
-
-
-
4
1
1
-
-
-
1
-
-
-
-
2
2
-
-
-