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Literature summary extracted from

  • Christian, T.; Sakaguchi, R.; Perlinska, A.; Lahoud, G.; Ito, T.; Taylor, E.; Yokoyama, S.; Sulkowska, J.; Hou, Y.
    Methyl transfer by substrate signaling from a knotted protein fold (2016), Nat. Struct. Mol. Biol., 23, 941-948 .
    View publication on PubMedView publication on EuropePMC

Application

EC Number Application Comment Organism
2.1.1.228 drug development TrmD is a leading antimicrobial drug target, due to its essentiality for bacterial growth, its broad conservation across bacterial species, and its deep-rooted distinction from the human and archaeal counterpart Trm5, which has the dinucleotide fold Haemophilus influenzae

Inhibitors

EC Number Inhibitors Comment Organism Structure
2.1.1.228 sinefungin
-
 Haemophilus influenzae

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.1.1.228 additional information Haemophilus influenzae TrmD is a bacterial enzyme with a trefoil-knot in the active site, involving three crossings of the protein backbone through a loop. TrmD catalyzes methyl transfer from AdoMet to the N1 of G37 on the 3' side of the tRNA anticodon ?
-
-
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA Haemophilus influenzae
-
 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.1.1.228 Haemophilus influenzae A0A0D0GZF5
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.1.1.228 additional information TrmD is a bacterial enzyme with a trefoil-knot in the active site, involving three crossings of the protein backbone through a loop. TrmD catalyzes methyl transfer from AdoMet to the N1 of G37 on the 3' side of the tRNA anticodon Haemophilus influenzae ?
-
-
2.1.1.228 S-adenosyl-L-methionine + guanine37 in tRNA
-
 Haemophilus influenzae S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?

Subunits

EC Number Subunits Comment Organism
2.1.1.228 More enzyme structures of apo- and binary tRNA-free forms, and of ternary complex including AdoMet, molecular dynamic analysis, simulations and modelling, overview. Molecular mechanics Poisson-Boltzmann surface area (MMPBSA) method Haemophilus influenzae

Synonyms

EC Number Synonyms Comment Organism
2.1.1.228 TrmD
-
 Haemophilus influenzae
2.1.1.228 tRNA(m(1)G37)methyltransferase
-
 Haemophilus influenzae

Cofactor

EC Number Cofactor Comment Organism Structure
2.1.1.228 S-adenosyl-L-methionine
-
 Haemophilus influenzae

General Information

EC Number General Information Comment Organism
2.1.1.228 evolution the TrmD knot is closely related to the trefoil-knot in SpoU methyl transferases, which catalyze 2'-O-methylation to RNA ribose for wide-ranging activities. In virtually all aspects of the methyl transfer reaction, TrmD is distinct from related Trm5 Haemophilus influenzae
2.1.1.228 malfunction elimination of TrmD increases protein synthesis frameshifts and causes cell death Haemophilus influenzae
2.1.1.228 additional information the structurally constrained TrmD knot is required for its catalytic activity. The TrmD knot has complex internal movements that respond to AdoMet binding and signaling. Most of the signaling propagates the free energy of AdoMet binding to stabilize tRNA binding and to assemble the active site. Principles of knots as an organized structure that captures the free energies of substrate binding to facilitate catalysis, overview Haemophilus influenzae
2.1.1.228 physiological function in bacteria, TrmD is a methyl transferase that uses a knotted protein fold to catalyze methyl transfer from S-adenosyl methionine (AdoMet) to G37-tRNA. The product m1G37-tRNA is essential for life as a determinant to maintain protein synthesis reading-frame Haemophilus influenzae