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Literature summary extracted from

  • Degut, C.; Ponchon, L.; Folly-Klan, M.; Barraud, P.; Tisne, C.
    The m1A58 modification in eubacterial tRNA: An overview of tRNA recognition and mechanism of catalysis by TrmI (2016), Biophys. Chem., 210, 27-34.
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.1.1.220 purified enzyme mutant D170A and Y78A in complex with S-adenosyl-L-methionine, hanging drop vapor diffusion method, mixing of 10 mg/ml protein in 20 mM Tris-HCl buffer, pH 8.0, 100 mM KCl, and 2mM S-adenosyl-L-methionine with reservoir solution containing 2.4 M ammonium sulfate and 10% v/v isopropanol for mutant D170A and 2.1 M ammonium sulfate and 8% v/v isopropanol for mutant Y78A, X-ray diffraction structure determination and analysis at 3.1 A and 2.6 A resolution, respectively. Crystallization assays of enzyme TrmI Y194A lead to poorly diffracting crystals Thermus thermophilus

Protein Variants

EC Number Protein Variants Comment Organism
2.1.1.220 D170A site-directed mutagenesis, mutation of a conserved active site residue Thermus thermophilus
2.1.1.220 Y194A site-directed mutagenesis, crystallization assays of TrmI Y194A lead to poorly diffracting crystals Thermus thermophilus
2.1.1.220 Y78A site-directed mutagenesis, mutation of a conserved active site residue. The structure of TrmI Y78A catalytic domain is unmodified regarding the binding of the SAM co-factor and the conformation of residues potentially interacting with the substrate adenine, as compared to the wild-type structure. The structure of the D170A mutant shows a flexible active site with one loop occupying in part the place of the co-factor and the second loop moving at the entrance to the active site Thermus thermophilus

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.1.1.220 S-adenosyl-L-methionine + adenine58 in tRNA Thermus thermophilus
-
 S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
-
 ?
2.1.1.220 S-adenosyl-L-methionine + adenine58 in tRNA Thermus thermophilus DSM 7039
-
 S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.1.1.220 Thermus thermophilus Q8GBB2 HB27
-
2.1.1.220 Thermus thermophilus DSM 7039 Q8GBB2 HB27
-

Reaction

EC Number Reaction Comment Organism Reaction ID
2.1.1.220 S-adenosyl-L-methionine + adenine58 in tRNA = S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA two possible mechanisms for methyl transfer: (A) with deprotonation of the amino exocyclic group of the adenine ring and via the intermediate imino tautomer of m1A, (B) by direct transfer of the methyl, without intermediate, detailed overview Thermus thermophilus
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.1.1.220 S-adenosyl-L-methionine + adenine58 in tRNA
-
 Thermus thermophilus S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
-
 ?
2.1.1.220 S-adenosyl-L-methionine + adenine58 in tRNA
-
 Thermus thermophilus DSM 7039 S-adenosyl-L-homocysteine + N1-methyladenine58 in tRNA
-
 ?

Synonyms

EC Number Synonyms Comment Organism
2.1.1.220 TrmI
-
 Thermus thermophilus

Cofactor

EC Number Cofactor Comment Organism Structure
2.1.1.220 S-adenosyl-L-methionine
-
 Thermus thermophilus

General Information

EC Number General Information Comment Organism
2.1.1.220 additional information recognition of tRNA substrate and structure of the catalytic pocket, overview. The flexibility of the N-terminal domain that is probably important to bind tRNA. Role of residue Y78 in stabilizing the conformation of the A58 ribose needed to hold substrate adenosine in the active site, and central role of residue D170 in binding the amino moiety of S-adenosyl-L-methionine and the exocyclic amino group of adenine Thermus thermophilus