2CNS

RimI - Ribosomal S18 N-alpha-protein acetyltransferase in complex with acetylCoA.

Summary for 2CNS

• Entry DOI: 10.2210/pdb2cns/pdb
• Related: 2CNM 2CNT
• Descriptor: MODIFICATION OF 30S RIBOSOMAL SUBUNIT PROTEIN S18, PHOSPHATE ION, ACETYL COENZYME *A, ... (4 entities in total)
• Functional Keywords: n-alpha acetylation, gcn5-n-acetyltransferase, ribosomal protein, acetyltransferase, gnat, transferase, acyltransferase
• Biological source: SALMONELLA TYPHIMURIUM LT2
• Total number of polymer chains: 3
• Total formula weight: 57690.91

Authors

Vetting, M.W.,Bareich, D.C.,Yu, M.,Blanchard, J.S. (deposition date: 2006-05-23, release date: 2007-06-19, Last modification date: 2024-05-08)

Primary citation

Vetting, M.W.,Bareich, D.C.,Yu, M.,Blanchard, J.S.
Crystal Structure of Rimi from Salmonella Typhimurium Lt2, the Gnat Responsible for N{Alpha}- Acetylation of Ribosomal Protein S18.
Protein Sci., 17:1781-1790, 2008

PubMed Abstract: 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.

PubMed: 18596200
DOI: 10.1110/PS.035899.108

Experimental method

X-RAY DIFFRACTION (2.5 Å)