Crystal structure of RimI from Salmonella typhimurium LT2, the GNAT responsible for N^α-acetylation of ribosomal protein S18

The three ribosomal proteins L7, S5, and S18 are included in the rare subset of prokaryotic proteins that are known to be N^α- acetylated. The GCN5-related N-acetyltransferase (GNAT) protein RimI, responsible for the N^α-acetylation of the ribosomal protein S18, was cloned from Salmonella typhimurium LT2 (RimI^ST), overexpressed, and purified to homogeneity. Steady-state kinetic parameters for RimI^ST were determined for AcCoA and a peptide substrate consisting of the first six amino acids of the target protein S18. The crystal structure of RimI^ST was determined in complex with CoA, AcCoA, and a CoA-S-acetyl-ARYFRR bisubstrate inhibitor. The structures are consistent with a direct nucleophilic addition-elimination mechanism with Glu103 and Tyr115 acting as the catalytic base and acid, respectively. The RimI^ST-bisubstrate complex suggests that several residues change conformation upon interacting with the N terminus of S18, including Glu103, the proposed active site base, facilitating proton exchange and catalysis.