Book of Abstracts: Albany 2005
A Model of Stop Codon Recognition in Eukariotes with Repulsive Guanine
Previously, we have advanced arguments that together with RF-factor a triplet CUA in the loop of the hairpin 69 of large rRNA participated in recognition of stop codons (Valery Ivanov, Artemy Beniaminov, Anrey Mikheyev, and Elvira Miniat. RNA 7, 1683-1692, 2001). This conservative triplet with the allowance of A-C pairing is able to recognize any of the three stop codons, UAA, UAG, UAA.
Figure below shows the structure of the stop codon recognition domain of the eRF1 factor. This is a sandwich structure with β-sheet with α-helices on the both sides. Also shown are Tyr125 and Cys 127, which are known to participate in recognition of Stops. The upper part of the Figure shows a known approximate position of Stops with the universal U near Lys 63. At the bottom part, please see CUA triplet, able to pair Stops. The triangles in the middle symbolize 2-aminogroups of Gs, if the guanines of Stops are present. These guanines according to my model are responsible for discrimination of G in stop codons in organisms (ciliates) with the restricted numbers of Stops, for example UAA, UAG (euplotes), UGA (tetrachymena).
The β-sheet is supposed to be able to make turn around the axis, indicated by a circle in the left part of the Figure.
It is suggested that in ?normal? eukaryotes (for example, H. sapiens, yeasts etc.) the above β-sheet (called ?Restrictor?) occupies an upper position. In this position no guanines of stops make clash to Tyr125 and Cys127, so that all the three Stops are recognizing. A turn to the middle position (as indicated in the Figure) the second G position brings the guanine into clash with Cys127. Thus, the Stop UGA will be discriminated (a case of euplotes, which recognize UAA and UAG). In the bottom position of Restrictor, the Tyr125 makes a clash with G in the third position, leaving UGA as the only Stop (tetrahymena). Here UAA and UAG code for glutamine.
(The detailed paper about eukariotic Stops recognition is under preparation.)
Valery I. Ivanov
The Engelhardt Institute of Molecular Biology