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show all sequences of 2.1.1.202

Substrate tRNA recognition mechanism of a multisite-specific tRNA methyltransferase, Aquifex aeolicus Trm1, based on the X-ray crystal structure

Awai, T.; Ochi, A.; Ihsanawati, A.; Sengoku, T.; Hirata, A.; Bessho, Y.; Yokoyama, S.; Hori, H.; J. Biol. Chem. 286, 35236-35246 (2011)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
gene MJ0026, expression in Escherichia coli strain BL21-CodonPlus(DE3)-RIL
Methanocaldococcus jannaschii
Crystallization (Commentary)
Crystallization
Organism
Trm4 free and in complex with sinefungin, hanging-drop vapor diffusion, 0.001 ml of protein solution containing 10.8 mg/ml protein with 0.001 ml of crystallization solution containing 100 mM Tris-HCl, pH 7.4, 200 mM MgCl2, 25% PEG 3350, and 6% v/v isopropanol for MJ0026 alone, and 20 100 mM Tris-HCl, pH 7.4, 200 mM MgCl2, 25% PEG 3350, 3 mM sinefungin, and 10 mM cytidine for Mj0026 with sinefungin, cryoprotectant 20% glycerol and 20% PEG 400, respectively, X-ray diffraction structure determination and analysis at 1.27 A and 2.3 A resolutions, respectively
Methanocaldococcus jannaschii
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
S-adenosyl-L-methionine + cytosine40 in tRNA precursor
Methanocaldococcus jannaschii
-
S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNA precursor
-
-
?
S-adenosyl-L-methionine + cytosine48 in tRNA
Methanocaldococcus jannaschii
-
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNA
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Methanocaldococcus jannaschii
-
gene MJ0026
-
Purification (Commentary)
Commentary
Organism
recombinant MJ0026 from Escherichia coli strain BL21-CodonPlus(DE3)-RIL by heat treatment, anion exchange and hydroxyapatite chromatography, and dialysis
Methanocaldococcus jannaschii
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
additional information
highly conserved residues form a large, positively charged surface, which seems to be suitable for tRNA binding. Substrate specificity and methylation sites on tRNA, overview
719968
Methanocaldococcus jannaschii
?
-
-
-
-
S-adenosyl-L-methionine + cytosine40 in tRNA precursor
-
719968
Methanocaldococcus jannaschii
S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNA precursor
-
-
-
?
S-adenosyl-L-methionine + cytosine48 in tRNA
-
719968
Methanocaldococcus jannaschii
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNA
-
-
-
?
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
70
-
assay at
Methanocaldococcus jannaschii
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.7
-
assay at
Methanocaldococcus jannaschii
Cofactor
Cofactor
Commentary
Organism
Structure
additional information
the S-adenosyl-L-methionine analigue sinefungin is bound in a negatively charged pocket near helix alpha8, binding structure, detailed overview
Methanocaldococcus jannaschii
S-adenosyl-L-methionine
helix alpha8 can adopt two different conformations, thereby controlling the entry of S-adenosyl-L-methionine into the active site
Methanocaldococcus jannaschii
Cloned(Commentary) (protein specific)
Commentary
Organism
gene MJ0026, expression in Escherichia coli strain BL21-CodonPlus(DE3)-RIL
Methanocaldococcus jannaschii
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
additional information
the S-adenosyl-L-methionine analigue sinefungin is bound in a negatively charged pocket near helix alpha8, binding structure, detailed overview
Methanocaldococcus jannaschii
S-adenosyl-L-methionine
helix alpha8 can adopt two different conformations, thereby controlling the entry of S-adenosyl-L-methionine into the active site
Methanocaldococcus jannaschii
Crystallization (Commentary) (protein specific)
Crystallization
Organism
Trm4 free and in complex with sinefungin, hanging-drop vapor diffusion, 0.001 ml of protein solution containing 10.8 mg/ml protein with 0.001 ml of crystallization solution containing 100 mM Tris-HCl, pH 7.4, 200 mM MgCl2, 25% PEG 3350, and 6% v/v isopropanol for MJ0026 alone, and 20 100 mM Tris-HCl, pH 7.4, 200 mM MgCl2, 25% PEG 3350, 3 mM sinefungin, and 10 mM cytidine for Mj0026 with sinefungin, cryoprotectant 20% glycerol and 20% PEG 400, respectively, X-ray diffraction structure determination and analysis at 1.27 A and 2.3 A resolutions, respectively
Methanocaldococcus jannaschii
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 + cytosine40 in tRNA precursor
Methanocaldococcus jannaschii
-
S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNA precursor
-
-
?
S-adenosyl-L-methionine + cytosine48 in tRNA
Methanocaldococcus jannaschii
-
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNA
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant MJ0026 from Escherichia coli strain BL21-CodonPlus(DE3)-RIL by heat treatment, anion exchange and hydroxyapatite chromatography, and dialysis
Methanocaldococcus jannaschii
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
additional information
highly conserved residues form a large, positively charged surface, which seems to be suitable for tRNA binding. Substrate specificity and methylation sites on tRNA, overview
719968
Methanocaldococcus jannaschii
?
-
-
-
-
S-adenosyl-L-methionine + cytosine40 in tRNA precursor
-
719968
Methanocaldococcus jannaschii
S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNA precursor
-
-
-
?
S-adenosyl-L-methionine + cytosine48 in tRNA
-
719968
Methanocaldococcus jannaschii
S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNA
-
-
-
?
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
70
-
assay at
Methanocaldococcus jannaschii
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.7
-
assay at
Methanocaldococcus jannaschii
Other publictions for EC 2.1.1.202
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)
735864
Burgess
Conservation of tRNA and rRNA ...
Arabidopsis thaliana, Brassica rapa, Caulerpa taxifolia, Ginkgo biloba, Nannochloropsis oculata, Triticum turgidum subsp. durum
BMC Plant Biol.
15
199
2015
-
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1
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-
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1
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6
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19
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1
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7
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6
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1
6
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1
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6
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1
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7
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-
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13
13
-
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-
735680
Moon
Trm4 and Nsun2 RNA:m5C methylt ...
Saccharomyces cerevisiae
Biochemistry
53
7132-7144
2014
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-
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1
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2
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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
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2
2
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-
735907
Hussain
NSun2-mediated cytosine-5 meth ...
Homo sapiens
Cell Rep.
4
255-261
2013
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-
-
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2
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10
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1
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1
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11
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1
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1
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2
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10
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1
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11
-
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1
2
2
1
-
-
736856
Khoddami
Identification of direct targe ...
Homo sapiens
Nat. Biotechnol.
31
458-464
2013
-
-
-
-
1
-
2
-
1
-
-
8
-
1
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4
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1
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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
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8
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1
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9
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-
-
2
2
-
-
-
737227
Preston
TRNAHis 5-methylcytidine level ...
Saccharomyces cerevisiae, Saccharomyces cerevisiae BY4741
RNA
19
243-256
2013
1
-
-
-
-
-
-
-
-
-
-
11
-
58
-
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13
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1
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1
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1
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-
11
-
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-
-
-
13
-
-
-
-
-
-
-
-
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1
3
3
1
-
-
719968
Awai
Substrate tRNA recognition mec ...
Methanocaldococcus jannaschii
J. Biol. Chem.
286
35236-35246
2011
-
-
1
1
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-
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-
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2
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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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2
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1
2
1
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2
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1
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3
-
1
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-
-
1
-
-
-
-
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-
-
-
-
710546
Walbott
Cysteine of sequence motif VI ...
Saccharomyces cerevisiae
RNA
13
967-973
2007
-
-
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-
1
-
-
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3
-
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1
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1
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1
-
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-
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-
672512
Redman
Assembly of protein-RNA comple ...
Saccharomyces cerevisiae
Biomacromolecules
7
3321-3326
2006
-
-
-
-
2
-
-
-
-
-
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2
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2
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-
-
-
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-
-
-
710135
Brzezicha
Identification of human tRNA:m ...
Saccharomyces cerevisiae
Nucleic Acids Res.
34
6034-6043
2006
-
-
1
-
-
-
-
-
-
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-
3
-
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3
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1
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1
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1
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3
-
1
-
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1
-
-
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-
-
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-
639472
King
RNA methyltransferases utilize ...
Saccharomyces cerevisiae
Biochemistry
41
11218-11225
2002
-
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2
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3
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1
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2
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1
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-
-
-
639471
Motorin
Multisite-specific tRNA:m5C-me ...
Saccharomyces cerevisiae
RNA
5
1105-1118
1999
-
-
1
-
-
-
-
-
-
-
3
4
-
4
-
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1
4
-
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8
1
1
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1
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1
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3
4
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1
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8
1
1
-
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1
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-
-
2
2
-
-
-
710134
Jiang
Pleiotropic effects of intron ...
Saccharomyces cerevisiae, Saccharomyces cerevisiae Pp1001
Nucleic Acids Res.
25
2694-2701
1997
-
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2
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4
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1
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1
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4
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1
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1
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-
709946
Strobel
Effect of intron mutations on ...
Saccharomyces cerevisiae
Mol. Cell. Biol.
6
2663-2673
1986
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1
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