Crystal structure of RimI from Salmonella typhimurium LT2, the GNAT responsible for N(alpha)-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(alpha)-acetylated. The GCN5-related N-acetyltransferase (GNAT) protein RimI, responsible for the N(alpha)-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.
Vetting
Matthew W
MW
Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
Bareich
David C
DC
Yu
Michael
M
Blanchard
John S
JS
D000107:Acetylation; D000123:Acetyltransferases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics; D003001:Cloning, Molecular; D003460:Crystallization; D018360:Crystallography, X-Ray; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D012269:Ribosomal Proteins / Q000378:metabolism*; D012486:Salmonella typhimurium / Q000201:enzymology*
D010455:Peptides; D012269:Ribosomal Proteins; C041184:ribosomal protein S18; D000123:Acetyltransferases