BRENDA - Enzyme Database
show all sequences of 2.1.1.228

Crystal structures of the bifunctional tRNA methyltransferase Trm5a

Wang, C.; Jia, Q.; Chen, R.; Wei, Y.; Li, J.; Ma, J.; Xie, W.; Sci. Rep. 6, 33553 (2016) View publication on PubMedView publication on EuropePMC

Data extracted from this reference:

Cloned(Commentary)
Cloned (Commentary)
Organism
gene trm5a, sequence comparisons, recombinant expression of N-terminally His6-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
Pyrococcus abyssi
Crystallization (Commentary)
Crystallization (Commentary)
Organism
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
Pyrococcus abyssi
Engineering
Protein Variants
Commentary
Organism
C301S/C308S/C326S
site-directed mutagenesis
Pyrococcus abyssi
V21C/C301S/C308S/K314C/C326S
site-directed mutagenesis
Pyrococcus abyssi
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Mg2+
required
Pyrococcus abyssi
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
additional information
Pyrococcus abyssi
bifunctional Trm5a from Pyrococcus abyssi (PaTrm5a) catalyses not only the methylation of N1, but also the further methylation of C7 on 4 demethylwyosine at position 37 to produce isowyosine (EC 2.1.1.228 and EC 2.1.1.282, respectively)
?
-
-
-
S-adenosyl-L-methionine + guanine37 in tRNAPhe
Pyrococcus abyssi
-
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAPhe
-
-
?
Organism
Organism
UniProt
Commentary
Textmining
Pyrococcus abyssi
Q9V2G1
-
-
Purification (Commentary)
Purification (Commentary)
Organism
recombinant N-terminally His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity and heparin affinity chromatography, and dialysis
Pyrococcus abyssi
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
additional information
bifunctional Trm5a from Pyrococcus abyssi (PaTrm5a) catalyses not only the methylation of N1, but also the further methylation of C7 on 4 demethylwyosine at position 37 to produce isowyosine (EC 2.1.1.228 and EC 2.1.1.282, respectively)
758376
Pyrococcus abyssi
?
-
-
-
-
additional information
substrate-binding modes of PaTrm5a, and recognition of substrate analogues, overview
758376
Pyrococcus abyssi
?
-
-
-
-
S-adenosyl-L-methionine + guanine37 in tRNAPhe
-
758376
Pyrococcus abyssi
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAPhe
-
-
-
?
Subunits
Subunits
Commentary
Organism
?
x * 38500, recombinant N-terminally His6-tagged enzyme, SDS-PAGE
Pyrococcus abyssi
More
enzyme structure analysis, the 38.5-kDa protein is composed of three domains: D1 (M1-P60), D2 (N70-S162) and D3 (K163-S333) D1 and D2 are connected through an interdomain linker (M61-K69), overview
Pyrococcus abyssi
Synonyms
Synonyms
Commentary
Organism
More
see also EC 2.1.1.282
Pyrococcus abyssi
PaTrm5a
-
Pyrococcus abyssi
TAW22
-
Pyrococcus abyssi
Trm5a
-
Pyrococcus abyssi
Cofactor
Cofactor
Commentary
Organism
Structure
S-adenosyl-L-methionine
-
Pyrococcus abyssi
Cloned(Commentary) (protein specific)
Commentary
Organism
gene trm5a, sequence comparisons, recombinant expression of N-terminally His6-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
Pyrococcus abyssi
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
S-adenosyl-L-methionine
-
Pyrococcus abyssi
Crystallization (Commentary) (protein specific)
Crystallization
Organism
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
Pyrococcus abyssi
Engineering (protein specific)
Protein Variants
Commentary
Organism
C301S/C308S/C326S
site-directed mutagenesis
Pyrococcus abyssi
V21C/C301S/C308S/K314C/C326S
site-directed mutagenesis
Pyrococcus abyssi
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Mg2+
required
Pyrococcus abyssi
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
additional information
Pyrococcus abyssi
bifunctional Trm5a from Pyrococcus abyssi (PaTrm5a) catalyses not only the methylation of N1, but also the further methylation of C7 on 4 demethylwyosine at position 37 to produce isowyosine (EC 2.1.1.228 and EC 2.1.1.282, respectively)
?
-
-
-
S-adenosyl-L-methionine + guanine37 in tRNAPhe
Pyrococcus abyssi
-
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAPhe
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant N-terminally His6-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity and heparin affinity chromatography, and dialysis
Pyrococcus abyssi
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
additional information
bifunctional Trm5a from Pyrococcus abyssi (PaTrm5a) catalyses not only the methylation of N1, but also the further methylation of C7 on 4 demethylwyosine at position 37 to produce isowyosine (EC 2.1.1.228 and EC 2.1.1.282, respectively)
758376
Pyrococcus abyssi
?
-
-
-
-
additional information
substrate-binding modes of PaTrm5a, and recognition of substrate analogues, overview
758376
Pyrococcus abyssi
?
-
-
-
-
S-adenosyl-L-methionine + guanine37 in tRNAPhe
-
758376
Pyrococcus abyssi
S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNAPhe
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
?
x * 38500, recombinant N-terminally His6-tagged enzyme, SDS-PAGE
Pyrococcus abyssi
More
enzyme structure analysis, the 38.5-kDa protein is composed of three domains: D1 (M1-P60), D2 (N70-S162) and D3 (K163-S333) D1 and D2 are connected through an interdomain linker (M61-K69), overview
Pyrococcus abyssi
General Information
General Information
Commentary
Organism
evolution
during the evolutionary process, some euryarchaeota like Thermococcus and Pyrococcus preserved both the trm5 genes from the crenarchaeal origin as well as the native copy, but others apparently lost the latter. Phylogenetic distribution analyses of trm5 homologues in archaeal genomes allow the identification of three archaeal Trm5 (aTrm5) subfamilies: Trm5a, Trm5b, and Trm5c. Trm5b refers to the native form, while Trm5a refers to the crenarchaeal origin, and Trm5c to other members with divergent Trm5 sequences11. The three Trm5s differ substantially in primary sequences
Pyrococcus abyssi
metabolism
the enzyme is part of the The biosynthetic pathway of mimG in Pyrococcus abyssi, overview. In archaea, G37 hypermodification in tRNAPhe leads to wyosine derivatives. They are important in reading-frame maintenance during protein synthesis, while the absence of such modifications results in elevated error rates in +1 frame-shifting. Among the modification products, 7-methylwyosine (mimG) is perhaps the earliest and minimalist version of the wyosine derivatives unique to some archaea, and 4-demethylwyosine (imG-14), isowyosine (imG2) have also been identified as intermediates along the pathway. The first biosynthetic step of mimG is the formation of m1G37, catalysed by the S-adenosine-L-methionine (SAM)-dependent tRNA methyltransferase named Trm5, which belongs to class-I methyltransferases. The second step is the complex radical-mediated formation of imG-14, catalyzed by the radical SAM enzyme Taw1. The Trm5 enzyme from the archaeon Pyrococcus abyssi (PaTrm5a) also catalyzes the methylation of C7 on imG-14 to produce imG2 (EC 2.1.1.282), which is further methylated on the N4 position of the imidazo-purine ring by Taw3 to form mimG
Pyrococcus abyssi
additional information
enzyme structure comparisons
Pyrococcus abyssi
physiological function
tRNA methyltransferase Trm5 catalyses the transfer of a methyl group from S-adenosyl-L-methionine to G37 in eukaryotes and archaea. The N1-methylated guanosine is the product of the initial step of the wyosine hypermodification, which is essential for the maintenance of the reading frame during translation. As a unique member of this enzyme family, Trm5a from Pyrococcus abyssi (PaTrm5a) catalyses not only the methylation of N1, but also the further methylation of C7 on 4-demethylwyosine at position 37 to produce isowyosine
Pyrococcus abyssi
General Information (protein specific)
General Information
Commentary
Organism
evolution
during the evolutionary process, some euryarchaeota like Thermococcus and Pyrococcus preserved both the trm5 genes from the crenarchaeal origin as well as the native copy, but others apparently lost the latter. Phylogenetic distribution analyses of trm5 homologues in archaeal genomes allow the identification of three archaeal Trm5 (aTrm5) subfamilies: Trm5a, Trm5b, and Trm5c. Trm5b refers to the native form, while Trm5a refers to the crenarchaeal origin, and Trm5c to other members with divergent Trm5 sequences11. The three Trm5s differ substantially in primary sequences
Pyrococcus abyssi
metabolism
the enzyme is part of the The biosynthetic pathway of mimG in Pyrococcus abyssi, overview. In archaea, G37 hypermodification in tRNAPhe leads to wyosine derivatives. They are important in reading-frame maintenance during protein synthesis, while the absence of such modifications results in elevated error rates in +1 frame-shifting. Among the modification products, 7-methylwyosine (mimG) is perhaps the earliest and minimalist version of the wyosine derivatives unique to some archaea, and 4-demethylwyosine (imG-14), isowyosine (imG2) have also been identified as intermediates along the pathway. The first biosynthetic step of mimG is the formation of m1G37, catalysed by the S-adenosine-L-methionine (SAM)-dependent tRNA methyltransferase named Trm5, which belongs to class-I methyltransferases. The second step is the complex radical-mediated formation of imG-14, catalyzed by the radical SAM enzyme Taw1. The Trm5 enzyme from the archaeon Pyrococcus abyssi (PaTrm5a) also catalyzes the methylation of C7 on imG-14 to produce imG2 (EC 2.1.1.282), which is further methylated on the N4 position of the imidazo-purine ring by Taw3 to form mimG
Pyrococcus abyssi
additional information
enzyme structure comparisons
Pyrococcus abyssi
physiological function
tRNA methyltransferase Trm5 catalyses the transfer of a methyl group from S-adenosyl-L-methionine to G37 in eukaryotes and archaea. The N1-methylated guanosine is the product of the initial step of the wyosine hypermodification, which is essential for the maintenance of the reading frame during translation. As a unique member of this enzyme family, Trm5a from Pyrococcus abyssi (PaTrm5a) catalyses not only the methylation of N1, but also the further methylation of C7 on 4-demethylwyosine at position 37 to produce isowyosine
Pyrococcus abyssi
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
-
-
-
736428
Masuda
The temperature sensitivity of ...
Escherichia coli
J. Biol. Chem.
288
28987-28996
2013
-
-
1
-
1
-
-
7
-
1
-
1
-
3
-
-
1
-
-
-
-
-
3
1
2
1
-
-
6
1
-
-
1
-
-
-
-
-
1
1
-
1
-
-
-
-
7
-
1
-
1
-
-
-
1
-
-
-
-
3
1
1
-
-
6
1
-
-
-
-
2
2
-
6
6
737226
Christian
Conservation of structure and ...
Homo sapiens
RNA
19
1192-1199
2013
-
-
1
-
9
-
-
3
-
-
-
1
-
12
-
-
1
1
-
-
-
-
2
-
1
1
-
-
1
1
1
-
1
-
-
-
-
-
1
1
-
9
-
-
-
-
3
-
-
-
1
-
-
-
1
-
-
-
-
2
-
1
-
-
1
1
1
-
-
-
2
2
-
1
1
737228
Paris
The T. brucei TRM5 methyltrans ...
Trypanosoma brucei brucei, Trametes pubescens 927 / 4 GUTat10.1 / TREU927
RNA
19
649-658
2013
-
-
1
-
1
-
-
-
2
-
-
2
-
5
-
-
1
-
-
-
-
-
12
-
1
-
-
-
-
-
-
-
1
-
-
-
-
-
1
1
-
1
-
-
-
-
-
2
-
-
2
-
-
-
1
-
-
-
-
12
-
-
-
-
-
-
-
-
-
-
2
2
-
-
-
721035
Sakaguchi
Recognition of guanosine by di ...
Escherichia coli, Methanocaldococcus jannaschii
RNA
18
1687-1701
2012
-
-
-
-
-
-
-
2
-
-
-
2
-
2
-
-
-
2
-
-
-
-
10
-
2
-
-
-
-
-
-
-
2
-
-
-
-
-
-
2
-
-
-
-
-
-
2
-
-
-
2
-
-
-
-
-
-
-
-
10
-
-
-
-
-
-
-
-
-
-
2
2
-
-
-
721029
Lahoud
Differentiating analogous tRNA ...
Escherichia coli, Methanocaldococcus jannaschii
RNA
17
1236-1246
2011
-
-
-
-
-
-
24
2
-
-
-
2
-
2
-
-
-
-
-
-
-
-
2
-
2
2
-
-
-
-
-
-
2
24
-
-
-
-
-
2
-
-
-
-
24
24
2
-
-
-
2
-
-
-
-
-
-
-
-
2
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
720240
Christian
Control of catalytic cycle by ...
Escherichia coli, Methanocaldococcus jannaschii
J. Mol. Biol.
400
204-217
2010
-
-
-
-
-
-
-
2
-
-
-
4
-
2
-
-
-
-
-
-
-
-
6
2
2
-
-
-
3
-
-
-
2
-
-
-
-
-
-
2
-
-
-
-
-
-
2
-
-
-
4
-
-
-
-
-
-
-
-
6
2
-
-
-
3
-
-
-
-
-
-
-
-
-
-
721026
Christian
Mechanism of N-methylation by ...
Methanocaldococcus jannaschii
RNA
16
2484-2492
2010
-
-
-
1
18
-
-
1
-
-
-
1
-
1
-
-
-
1
-
1
-
-
3
-
2
1
-
-
-
-
1
-
1
-
-
-
-
-
-
1
1
18
-
-
-
-
1
-
-
-
1
-
-
-
-
-
1
-
-
3
-
1
-
-
-
-
1
-
-
-
-
-
-
-
-
701123
Goto-Ito
Crystal structure of archaeal ...
Methanocaldococcus jannaschii
Proteins
72
1274-1289
2008
-
-
-
1
-
-
1
1
-
-
-
-
-
11
-
-
-
-
-
-
-
-
1
-
2
1
-
-
1
1
-
-
-
-
-
-
-
-
-
-
1
-
-
-
1
-
1
-
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
1
1
-
-
-
-
-
-
-
1
1
712103
Toyooka
Stabilization of tRNA (mG37) m ...
Aquifex aeolicus
Genes Cells
13
807-816
2008
-
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
1
-
-
-
-
-
-
-
1
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
687609
Lee
Yeast mitochondrial initiator ...
Saccharomyces cerevisiae
J. Biol. Chem.
282
27744-27753
2007
-
-
1
-
-
-
-
-
2
-
-
1
-
2
-
-
1
-
-
-
-
-
2
-
1
1
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
2
-
-
1
-
-
-
1
-
-
-
-
2
-
1
-
-
-
1
-
-
-
-
2
2
-
-
-
712739
Christian
Distinct determinants of tRNA ...
Escherichia coli, Methanocaldococcus jannaschii
J. Mol. Biol.
373
623-632
2007
-
-
-
-
-
-
-
5
-
-
-
2
-
2
-
-
-
-
-
-
-
-
5
-
2
2
-
-
5
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
5
-
-
-
2
-
-
-
-
-
-
-
-
5
-
2
-
-
5
2
-
-
-
-
2
2
-
5
5
673850
Takeda
The substrate specificity of t ...
Aquifex aeolicus
Genes Cells
11
1353-1365
2006
-
-
1
-
-
-
-
13
-
-
-
1
-
6
-
-
1
-
-
-
-
-
15
-
3
1
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
13
-
-
-
1
-
-
-
1
-
-
-
-
15
-
1
-
-
-
1
-
-
-
-
-
-
-
-
-
711197
Christian
Catalysis by the second class ...
Methanocaldococcus jannaschii
Biochemistry
45
7463-7473
2006
-
-
-
-
9
-
-
11
-
-
-
-
-
1
-
-
1
-
-
-
-
-
1
-
2
1
-
-
11
1
-
-
-
-
-
-
-
-
-
-
-
9
-
-
-
-
11
-
-
-
-
-
-
-
1
-
-
-
-
1
-
1
-
-
11
1
-
-
-
-
1
1
-
11
11
661154
Brule
Isolation and characterization ...
Escherichia coli, Homo sapiens
Biochemistry
43
9243-9255
2004
1
-
2
-
-
-
5
13
-
3
2
2
-
9
-
-
2
-
-
-
-
-
20
2
4
2
-
-
-
4
2
-
-
-
-
-
1
-
2
-
-
-
-
-
5
-
13
-
3
2
2
-
-
-
2
-
-
-
-
20
2
2
-
-
-
4
2
-
-
-
-
-
-
-
-
662010
O'Dwyer
Characterization of Streptococ ...
Streptococcus pneumoniae
J. Bacteriol.
186
2346-2354
2004
-
-
1
-
-
-
-
2
-
4
3
1
-
5
-
-
1
-
-
-
-
-
3
1
1
1
-
-
2
2
1
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
2
-
4
3
1
-
-
-
1
-
-
-
-
3
1
1
-
-
2
2
1
-
-
-
-
-
-
2
2
662622
Christian
Distinct origins of tRNA(m1G37 ...
Methanocaldococcus jannaschii
J. Mol. Biol.
339
707-719
2004
-
1
1
-
5
-
-
-
-
-
1
-
-
6
-
-
1
-
-
-
-
-
7
1
3
1
-
-
-
-
-
-
-
-
-
-
-
1
1
-
-
5
-
-
-
-
-
-
-
1
-
-
-
-
1
-
-
-
-
7
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
661585
Ahn
Crystal structure of tRNA(m1G3 ...
Haemophilus influenzae
EMBO J.
22
2593-2603
2003
-
-
-
1
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
1
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
1
1
-
-
-
712737
Elkins
Insights into catalysis by a k ...
Escherichia coli
J. Mol. Biol.
333
931-949
2003
-
-
1
1
44
-
-
-
-
-
2
-
-
3
-
-
1
-
-
-
-
-
-
1
2
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
1
44
-
-
-
-
-
-
-
2
-
-
-
-
1
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
713482
Liu
Crystal structure of tRNA (m1G ...
Aquifex aeolicus
Proteins
53
326-328
2003
-
-
-
1
-
-
-
-
-
-
-
-
-
3
-
-
-
-
-
-
-
-
-
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
1
1
-
-
-
710708
Kim
Crystallization and preliminar ...
Haemophilus influenzae
Acta Crystallogr. Sect. D
59
183-184
2002
-
-
1
1
-
-
-
-
-
-
-
-
-
6
-
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-