The structures of A and P product analogues and substrate are refined at 3 A resolution. At the same time, there is an intermediate analogue which is bound to a Haloarcula subunit of marismortui 50 S ribosomes. CCA-Phe-caproic acid-biotin and AP site substrate bind equitably to both sites. However, the introduction of sparsomycin makes the binding only to P site. CCA pieces of these analogues bind similarly by P or A loop of the tRNA.
When the separate A and P site forms combine, there is a complex single model that also reveals unique interactions. This is especially true when the two sites are introduced simultaneously. For example, there is formation of one hydrogen bond from the N3 of A2486. There could be a second bond of hydrogen. The amino group then positions itself adjacent to carbonyl carbon of P and the site makes a suitable orientation for an attack of nucleophilia.
Canada peptide acknowledges an important thing – the initial evolutionary instance in the introduction of the protein world from a RNA world was the appearance of enzymes that could catalyze the formation of peptide bonds. There are two major components at the peptidyl transfer center.
This is the large ribosomal unit where the synthesis of peptide bond happens. One of these two components is an interaction of A site with CCA end of aminoacylated tRNAs. The other component is a P site in which the CCA ends of peptidyl RNAs bind upon the formation of peptide bonds. Next, it catalyzes a reaction called a nucleophilic attack. This is the amino group attack of aminoacyl tRNA that is bound to the A site.
The carbonyl carbon of ester bond linked to a tRNA blossoming peptide in the P site. We seek to address the following question. How does the ribosome enhance the peptide bond formation rate yet it is an RNA-protein machine whose roots are in the RNA world?