NpmA is a plasmid-mediated methyltransferase that was discovered in Japan, 2003, and confers a high level of aminoglycoside antibiotic resistance against most antibiotics in- class. It is active as a monomer in solution but is known to dimerize as well. NpmA uses an S-adenosyl-methionine (SAM) as cofactor to remove a methyl group from SAM, converting it to S-adenosyl-homocysteine (SAH), and add it to the 30S ribosome unit on adenosine 1408. This addition prevents the binding of aminoglycosides and blocks their ability to shut down the ribosome and RNA transcription.[1]
RNA Stabilization
Around the active site for NpmA, there are certain regions that help in stabilizing the RNA. One such region involves W107 and W197, which uses aromatic stacking with the tryptophans' indole groups to stabilize A1408 of the RNA. Another region that assists in RNA stabilization is F62-F82. This region utilizes four positive lysine residues to hold onto the negative charge of the RNA.[2]
Co-Factor Stabilization
S-Adenosylmethionine
SAM binding pocket uses hydrogen bonding interactions between residues N38, D55, A87, E88, T109, L104, and S195. Alanine and lysine use backbone residues for hydrogen bonding.[1]
SAH binding pocket utilizes hydrogen bonding with key residues such as D30, D55, A87, E88, L104, and T109. The alanine and lysine residues participate in hydrogen bonding with their backbone atoms.[1]
Many proteins that have similar sequences and functions to NpmA differ in where the key residues occur. For example, KamB is another SAM-dependent methyltransferase that methylates A1408 on the 30s subunit.[3] KamB does have the RNA stabilizing tryptophan residues, but they are W105 and W193 which indicates that there are two residues that are likely missing from KamB that are in NpmA. This is common across many similar proteins to NpmA.
[1]Nilofer Husain, Sonja Obranić, Lukasz Koscinski, J. Seetharaman, Fedora Babić, Janusz M. Bujnicki, Gordana Maravić-Vlahoviček, J. Sivaraman, Structural basis for the methylation of A1408 in 16S rRNA by a panaminoglycoside resistance methyltransferase NpmA from a clinical isolate and analysis of the NpmA interactions with the 30S ribosomal subunit, Nucleic Acids Research, Volume 39, Issue 5, 1 March 2011, Pages 1903–1918, https://doi.org/10.1093/nar/gkq1033.
[2]Husain, N., Tulsian, N., Chien, W. et al. Ligand-mediated changes in conformational dynamics of NpmA: implications for ribosomal interactions. Sci Rep 6, 37061 (2016). https://doi.org/10.1038/srep37061.
[3]Kawai A, Suzuki M, Tsukamoto K, Minato Y, Doi Y,, 2021. Functional and Structural Characterization of Acquired 16S rRNA Methyltransferase NpmB1 Conferring Pan-Aminoglycoside Resistance. Antimicrob Agents Chemother 65:10.1128/aac.01009-21.
