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Literature summary for 2.1.1.228 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
Search for more literature for 2.1.1.228

Application

Application Comment Organism
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

Inhibitors Comment Organism Structure
sinefungin
-
 Haemophilus influenzae

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
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 ?
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-
S-adenosyl-L-methionine + guanine37 in tRNA Haemophilus influenzae
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 S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?

Organism

Organism UniProt Comment Textmining
Haemophilus influenzae A0A0D0GZF5
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-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
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 ?
-
-
S-adenosyl-L-methionine + guanine37 in tRNA
-
 Haemophilus influenzae S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
-
 ?

Subunits

Subunits Comment Organism
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

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

Cofactor

Cofactor Comment Organism Structure
S-adenosyl-L-methionine
-
 Haemophilus influenzae

General Information

General Information Comment Organism
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
malfunction elimination of TrmD increases protein synthesis frameshifts and causes cell death Haemophilus influenzae
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
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