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Crystal structure of RimI from Salmonella typhimurium LT2 , the GNAT responsible for N α ‐acetylation of ribosomal protein S18
Author(s) -
Vetting Matthew W.,
Bareich David C.,
Yu Michael,
Blanchard John S.
Publication year - 2008
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.035899.108
Subject(s) - acetylation , ribosomal protein , salmonella , ribosomal rna , chemistry , active site , biochemistry , amino acid , stereochemistry , enzyme , biology , gene , bacteria , genetics , ribosome , rna
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.