Mechanism of decoding mRNA in protein biosynthesis

Various experimental data have been supporting an idea that the conformation of A-site tRNA is different from that of P-site tRNA and have led to a new tRNA docking pair model, in which the highly conserved G18 and G19 of D-loop in A-site tRNA and C56 and C61 of T Psi C-loop in P-site tRNA base pair exist along with the conventional base pairs of adjacent codon-anticodon interactions. This A-P tRNA pair model can be translocated to the P-E tRNA model without changing the conformation except the ACCA termini, keeping the position of the growing nascent polypeptide chain. On the other hand, it is noteworthy that C1378 of E. coli 16S rRNA cross-links to the 32 position on the anticodon loop of A-site tRNA in the pre-translocational state, and also to the same position of E-site tRNA in the post-translocational state, instead of the corresponding position of P-site tRNA. It resulted in a relationship between the A-P and P-E tRNA docking pair models in the pre-and post-translocational states, respectively, caused by a rotation with the angle of 25 degrees around the axis of rotation symmetry. Furthermore, nucleotide sequence analysis showed that CGAGC1107 of 16S rRNA is complementary with the conserved GT Psi CG57 of tRNA. When it is combined with the P-E tRNA pair model, the crystallographically obtained L-shaped tRNA model fits both A-site codon with base pairings and the free T Psi C-loop of P-site tRNA without base pairings. The base pairings between the GT Psi CG57 of tRNA and the CGAGC1107 of 16S rRNA destabilize the bound aminoacyl-tRNA and result in a flow of discarding noncognate and near-cognate ternary complexes until cognate one arrives at the A-site codon. Recognition of a cognate ternary complex could occur, starting from breaking a hydrogen bond between N3 atom of U33 and O5' atom of A36 in the aminoacyl-tRNA, with base pairings of the codon-anticodon interactions, the conserved A 1394 in the 16S rRNA to the conserved U33 in the anticodon loop of the tRNA. The exposed U33 of the aminoacyl-tRNA is paired with A1394 in the recognition mode of A site, and finally passed to A1398 of A-site tRNA in the A-P tRNA pair model of the pre-translocational state. The exposure of U33 base at the A site is a key event in the mechanism of codon recognition.