The kink-turn: a new RNA secondary structure motif
Abstract
Analysis of the Haloarcula marismortui large ribosomal subunit has revealed a common RNA structure that we call the kink-turn, or K-turn. The six K-turns in H.marismortui 23S rRNA superimpose with an r.m.s.d. of 1.7 Å. There are two K-turns in the structure of Thermus thermophilus 16S rRNA, and the structures of U4 snRNA and L30e mRNA fragments form K-turns. The structure has a kink in the phosphodiester backbone that causes a sharp turn in the RNA helix. Its asymmetric internal loop is flanked by C–G base pairs on one side and sheared G–A base pairs on the other, with an A-minor interaction between these two helical stems. A derived consensus secondary structure for the K-turn includes 10 consensus nucleotides out of 15, and predicts its presence in the 5′-UTR of L10 mRNA, helix 78 in Escherichia coli 23S rRNA and human RNase MRP. Five K-turns in 23S rRNA interact with nine proteins. While the observed K-turns interact with proteins of unrelated structures in different ways, they interact with L7Ae and two homologous proteins in the same way.
Acknowledgements
The authors wish to thank Poul Nissen, Nenad Ban, Jeff Hansen and Lara Weinstein for many helpful discussions, and Joe Ippolito and Satwik Kamtekar for critical reading of the manuscript. D.J.K. is an HHMI predoctoral fellow. This work was supported by NIH grants GM22778 to T.A.S. and GM54216 to P.B.M., as well as by a grant from the Agouron Institute. The full coordinates of the refined structure of the H.marismortui 50S subunit have been deposited in the Protein Data Bank with accession number 1JJ2.