An Archaeal Dim2-Like Protein, aDim2p, Forms a Ternary Complex with a/eIF2α and the 3′ End Fragment of 16S rRNA

Dim2p is a eukaryal small ribosomal subunit RNA processing factor required for the maturation of 18S rRNA. Here we show that an archaeal homolog of Dim2p, aDim2p, forms a ternary complex with the archaeal homolog of eIF2α, a/eIF2α, and the RNA fragment that possesses the 3′ end sequence of 16S rRNA both in solution and in crystal. The 2.8-Å crystal structure of the ternary complex reveals that two KH domains of aDim2p, KH-1 and -2, are involved in binding the anti-Shine–Dalgarno core sequence (CCUCC-3′) and a highly conserved adjacent sequence (5′-GGAUCA), respectively, of the target rRNA fragment. The surface plasmon resonance results show that the interaction of aDim2p with the target rRNA fragment is very strong, with a dissociation constant of 9.8 × 10− 10 M, and that aDim2p has a strong nucleotide sequence preference for the 3′ end sequence of 16S rRNA. On the other hand, aDim2p interacts with the isolated α subunit and the intact αβγ complex of a/eIF2, irrespective of the RNA binding. These results suggest that aDim2p is a possible archaeal pre-rRNA processing factor recognizing the 3′ end sequence (5′-GAUCACCUCC-3′) of 16S rRNA and may have multiple biological roles in vivo by interacting with other proteins such as a/eIF2 and aRio2p.