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Crystal Structure of RimI from Salmonella typhimurium LT2, the GNAT responsible for N-acetylation of Ribosomal Protein S18

Albert Einstein College of Medicine

(RECEIVED April 17, 2008; ACCEPTED June 20, 2008)

The three ribosomal proteins L7, S5 and S18 are included in the rare subset of prokaryotic proteins that are known to be N-acetylated. The GCN5-related N-acetyltransferase (GNAT) protein RimI, responsible for the N-acetylation of the ribosomal protein S18, was cloned from Salmonella typhimurium LT2 (RimIST), overexpressed and purified to homogeneity. Steady state kinetic parameters for RimIST were determined for AcCoA and a peptide substrate consisting of the first 6 amino acids of the target protein S18. The crystal structure of RimIST 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 RimIST-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.

Keywords: Conformational changes; Enzymes; Crystallography; Protein Sequencing, Modification, Mass Spectroscopy; Mechanism - Enzymes

¹ E-mail: blanchar{at}aecom.yu.edu

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