Structural Implications of Universal Complementarities in Translation—High Accuracy at the Decoding Site

Abstract

X-ray structures of transfer RNAs (tRNAs) bound to the whole ribosome do not fully explain the mechanism of translation. The cause of the failure seems to come mainly from a high Mg 2+ ion concentration compared to that in the living cells. There exists a wide range of nucleotide sequence conservation in tRNA and ribosomal RNAs (rRNAs) of small and large subunits as well as sequence complementarities that seems to explain how high accuracy in translation can be achieved at the decoding site. Conformational transition between U33-folded and U33-extended forms of anticodon loops of tRNAs and G-C pair formation and disruption between C1399 and G1504 of 16S rRNA, etc. play the central role in explaining why E-site tRNA can automatically be expelled when an aminoacyl-tRNA at the A site turns out to be cognate.

Abiogenic evolution of ribonucleic acid as a left-handed helix and its protecting substances on primordial earth – A story about evolution of ribosome and the origin of life

“…On the other hand, Nagano (2015) demonstrated a different type of P/A-and E/P-kinks, as shown in Figure 49, each of which is supported by one cluster of Mg 2+ hexahydrate. The difference of the kink structures of Nagano [9] from those in the X-ray structures can be rationalized on …”

“…It is known that U33 is highly conserved for all tRNAs. The anticodon loop holds in its crystal structure a magnesium ion in the pocket, but under a low magnesium concentration of 1 mMol, that is about the same as that of outside the cell, the loop behaves much more flexible than that of crystalline form [9]. This is one of the most important point in the evolution of life for capability of selection for all L-amino acids and glycine in its pocket.…”

“…At this stage of evolution of life. The nucleotide at the 33th position might not have to be uridine, but U33 seems more favorable for performing a multifunctional role in translation [9].…”

“…In contrast to the X-ray structure of the elbow region of the isolated L-form tRNA, in which G19 is paired with C56 as a Watson-Crick type, but G18 is hydrogen-bonded to Ѱ55 in an irregular fashion [8], the universally conserved guanines, G18 and G19, of aa-tRNA at the T site are base-paired with the other universally conserved cytidines, C56 and C61, of P-site tRNA, respectively, and also G18 and G19 of P-site tRNA with C56 and C61 of E-site tRNA, respectively. Such a big difference in the shape of tRNA between the isolated L-form of X-ray structure [8, 21,26] and the docking model of Nagano et al [29] as well as Nagano [9] comes from a big difference in the Mg 2+ concentration, as mentioned above.…”

“…It seemed possible for either A1502 or A1503 with U33 of the U33-extended form of deacylated tRNA at the E site. The result of the model building of Nagano (2015) has shown that A1502 is most favorable, while A1503 seems a little too far from the U33 of E-site tRNA. GUCAGCUCGUGCGU CGAGC UAGUACGAGAGGAU 1 1 0 0 GUCAGCUCGUGCGU CGAGC UAGUACGAGAGGAC 0 0 0 0 GUCAGCUCGUGUCG CGAGC UUGUACGAGAGGAC 7 0 1 0 GUCAGCUCGUGUCU CGAGC UAGUACGAGAGGAC 22 10 1 0 GUCAGCUCGUGUCG CGAGC UAGUACGAGAGGAC 14 …”