1VQM

The structure of the transition state analogue "DAN" bound to the large ribosomal subunit of haloarcula marismortui

Summary for 1VQM

• Entry DOI: 10.2210/pdb1vqm/pdb
• Related: 1FFK 1FFZ 1FGO 1JJ2 1KQS 1M90 1Q7Y 1Q81 1Q82 1Q86 1QVF 1QVG 1S72 1VQ4 1VQ5 1VQ6 1VQ7 1VQ8 1VQ9 1VQK 1VQL 1VQN 1VQO 1VQP
• Descriptor: 23S ribosomal rna, ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG, 50S RIBOSOMAL PROTEIN L10E, ... (39 entities in total)
• Functional Keywords: ribosome 50s, protein-protein complex, rna-rna complex, protein-rna complex, peptidyl transferase reaction, ribosome
• Biological source: Haloarcula marismortui; More
• Total number of polymer chains: 32
• Total formula weight: 1490916.75

Authors

Schmeing, T.M.,Steitz, T.A. (deposition date: 2004-12-16, release date: 2005-11-29, Last modification date: 2023-08-23)

Primary citation

Schmeing, T.M.,Huang, K.S.,Kitchen, D.E.,Strobel, S.A.,Steitz, T.A.
Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction.
Mol.Cell, 20:437-448, 2005

PubMed Abstract: Peptide bond formation is catalyzed at the peptidyl transferase center (PTC) of the large ribosomal subunit. Crystal structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with several analogs that represent either the substrates or the transition state intermediate of the peptidyl transferase reaction show that this reaction proceeds through a tetrahedral intermediate with S chirality. The oxyanion of the tetrahedral intermediate interacts with a water molecule that is positioned by nucleotides A2637 (E. coli numbering, 2602) and (methyl)U2619(2584). There are no Mg2+ ions or monovalent metal ions observed in the PTC that could directly promote catalysis. The A76 2' hydroxyl of the peptidyl-tRNA is hydrogen bonded to the alpha-amino group and could facilitate peptide bond formation by substrate positioning and by acting as a proton shuttle between the alpha-amino group and the A76 3' hydroxyl of the peptidyl-tRNA.

PubMed: 16285925
DOI: 10.1016/j.molcel.2005.09.006

Experimental method

X-RAY DIFFRACTION (2.3 Å)