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. 2001 Apr 24;98(9):4899-903.
doi: 10.1073/pnas.081082398. Epub 2001 Apr 10.

RNA tertiary interactions in the large ribosomal subunit: the A-minor motif

P Nissen  1 , J A Ippolito, N Ban, P B Moore, T A Steitz
Affiliations

RNA tertiary interactions in the large ribosomal subunit: the A-minor motif

P Nissen et al. Proc Natl Acad Sci U S A. .

Abstract

Analysis of the 2.4-A resolution crystal structure of the large ribosomal subunit from Haloarcula marismortui reveals the existence of an abundant and ubiquitous structural motif that stabilizes RNA tertiary and quaternary structures. This motif is termed the A-minor motif, because it involves the insertion of the smooth, minor groove edges of adenines into the minor groove of neighboring helices, preferentially at C-G base pairs, where they form hydrogen bonds with one or both of the 2' OHs of those pairs. A-minor motifs stabilize contacts between RNA helices, interactions between loops and helices, and the conformations of junctions and tight turns. The interactions between the 3' terminal adenine of tRNAs bound in either the A site or the P site with 23S rRNA are examples of functionally significant A-minor interactions. The A-minor motif is by far the most abundant tertiary structure interaction in the large ribosomal subunit; 186 adenines in 23S and 5S rRNA participate, 68 of which are conserved. It may prove to be the universally most important long-range interaction in large RNA structures.

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Figures

Figure 1
Figure 1
(a) The smooth minor groove face of the adenosine nucleotide allows the base to pack tightly into the minor groove of an RNA helix. Its N1, N3, and 2′-OH atoms are available for hydrogen-bonding interactions. (b) Ribbon drawing of the overall structure of the 50S ribosomal subunit from H. marismortui highlighting the 186 adenosines (shown in red spheres) that make A-minor interactions based on distance and geometric criteria (see text). (c) Examples of the four major types of A-minor interactions found in H. marismortui 50S shown in surface representation. Each type is defined by the position of the 2′-OH group of the interacting adenosine relative to the positions of the two 2′-OH groups of the receptor base pair. Whereas type I and type II interactions are A-specific, type 0 and type III also are observed for other bases even though As are still preferred when the base packs against the ribose backbone.
Figure 2
Figure 2
Examples of RNA tertiary structure stabilization by A-minor interactions in H. marismortui 23S rRNA. (a) A-minor interactions play an important role in stabilizing the interaction between helix 68 of domain IV (yellow and green), which forms the front rim of the active site cleft and helix 75 of domain V (blue). Four adenosines from two opposing strands of helix 68 (colored red) are stacked to allow packing within the minor groove of helix 75. (b) A-minor interactions (shown in red) are also critical in mediating loop–loop interactions, such as the one observed between the stem loops of helices 66 (blue) and 52 (yellow), and loop–helix interactions as the one observed between the helix 52 stem loop (yellow) and helix 11 (green). (c) The single-stranded junction between helices 41 and 42 (J41.42; yellow) donates adenosine residues for A-minor interactions that stabilize the interaction between helix 89 (green) and helix 90 (blue).
Figure 3
Figure 3
(a) Interaction between the A patch on helix 2 (in yellow stick) with the minor groove of helix 26 (shown in surface representation). A519, A520, and A521 of helix 2 make type III, type II, and type I interactions, respectively, typical of A-patch packing geometry in the A-minor motif. (b) 5S rRNA solely interacts with 23S rRNA via a symmetric A-patch interaction between three stacked adenosines of the 5S rRNA loop E helix and three stacked adenosines in helix 38 of 23S rRNA.
Figure 4
Figure 4
(a) Structure of a peptidyl transferase transition state analogue (29) (yellow) bound to the active site of the 50S ribosomal subunit of H. marismortui (in green). Each of the adenosine-like groups on the inhibitor that are analogous to A76 residues of the P-site and A-site tRNAs (with base planes in red) make type I A-minor interactions with base pairs in domain V of 23S rRNA. (b) The interaction between ribosomal protein L6 (yellow) and 23S rRNA is mediated by conserved A patches (shown in red space filling) on helix 95 (orange) and helix 97 (green).
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