Publications

• The YqfN protein of Bacillus subtilis is the tRNA: m1A22 methyltransferase (TrmK).

  Roovers M., Kaminska K.H., Tkaczuk K.L., Gigot D., Droogmans L., Bujnicki J.M.

  N(1)-methylation of adenosine to m(1)A occurs in several different positions in tRNAs from various organisms. A methyl group at position N(1) prevents Watson-Crick-type base pairing by adenosine and is therefore important for regulation of structure and stability of tRNA molecules. Thus far, only ... >> More

  N(1)-methylation of adenosine to m(1)A occurs in several different positions in tRNAs from various organisms. A methyl group at position N(1) prevents Watson-Crick-type base pairing by adenosine and is therefore important for regulation of structure and stability of tRNA molecules. Thus far, only one family of genes encoding enzymes responsible for m(1)A methylation at position 58 has been identified, while other m(1)A methyltransferases (MTases) remain elusive. Here, we show that Bacillus subtilis open reading frame yqfN is necessary and sufficient for N(1)-adenosine methylation at position 22 of bacterial tRNA. Thus, we propose to rename YqfN as TrmK, according to the traditional nomenclature for bacterial tRNA MTases, or TrMet(m(1)A22) according to the nomenclature from the MODOMICS database of RNA modification enzymes. tRNAs purified from a DeltatrmK strain are a good substrate in vitro for the recombinant TrmK protein, which is sufficient for m(1)A methylation at position 22 as are tRNAs from Escherichia coli, which natively lacks m(1)A22. TrmK is conserved in Gram-positive bacteria and present in some Gram-negative bacteria, but its orthologs are apparently absent from archaea and eukaryota. Protein structure prediction indicates that the active site of TrmK does not resemble the active site of the m(1)A58 MTase TrmI, suggesting that these two enzymatic activities evolved independently. << Less

  Nucleic Acids Res. 36:3252-3262(2008) [PubMed] [EuropePMC]

• Crystal structure of Streptococcus pneumoniae Sp1610, a putative tRNA methyltransferase, in complex with S-adenosyl-L-methionine.

  Ta H.M., Kim K.K.

  Streptococcus pneumoniae Sp1610, a Class-I fold S-adenosylmethionine (AdoMet)-dependent methyltransferase, is a member of the COG2384 family in the Clusters of Orthologous Groups database, which catalyzes the methylation of N(1)-adenosine at position 22 of bacterial tRNA. We determined the crystal ... >> More

  Streptococcus pneumoniae Sp1610, a Class-I fold S-adenosylmethionine (AdoMet)-dependent methyltransferase, is a member of the COG2384 family in the Clusters of Orthologous Groups database, which catalyzes the methylation of N(1)-adenosine at position 22 of bacterial tRNA. We determined the crystal structure of Sp1610 in the ligand-free and the AdoMet-bound forms at resolutions of 2.0 and 3.0 A, respectively. The protein is organized into two structural domains: the N-terminal catalytic domain with a Class I AdoMet-dependent methyltransferase fold, and the C-terminal substrate recognition domain with a novel fold of four alpha-helices. Observations of the electrostatic potential surface revealed that the concave surface located near the AdoMet binding pocket was predominantly positively charged, and thus this was predicted to be an RNA binding area. Based on the results of sequence alignment and structural analysis, the putative catalytic residues responsible for substrate recognition are also proposed. << Less

  Protein Sci 19:617-624(2010) [PubMed] [EuropePMC]