Summary information and primary citation
- PDB-id
-
1vqm;
DSSR-derived features in text and
JSON formats
- Class
- ribosome
- Method
- X-ray (2.3 Å)
- Summary
- The structure of the transition state analogue "dan"
bound to the large ribosomal subunit of haloarcula
marismortui
- Reference
-
Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz TA
(2005): "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. doi: 10.1016/j.molcel.2005.09.006.
- 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.
