Crystal Structure of a Model Branchpoint-U2 SnRNA Duplex Containing Bulged Adenosines

Overview

Journal RNA

Specialty Molecular Biology

Date 2001 May 15

PMID 11350032

Citations 29

Authors

J A Berglund

M Rosbash

S C SCHULTZ

Affiliations

Soon will be listed here.

Abstract

Bulged nucleotides play a variety of important roles in RNA structure and function, frequently forming tertiary interactions and sometimes even participating in RNA catalysis. In pre-mRNA splicing, the U2 snRNA base pairs with the intron branchpoint sequence (BPS) to form a short RNA duplex that contains a bulged adenosine that ultimately serves as the nucleophile that attacks the 5' splice site. We have determined a 2.18-A resolution crystal structure of a self-complementary RNA designed to mimic the highly conserved yeast (Saccharomyces cerevisiae) branchpoint sequence (5'-UACUAACGUAGUA with the BPS italicized and the branchsite adenosine underlined) base paired with its complementary sequence from U2 snRNA. The structure shows a nearly ideal A-form helix from which two unpaired adenosines flip out. Although the adenosine adjacent to the branchsite adenosine is the one bulged out in the structure described here, either of these adenosines can serve as the nucleophile in mammalian but not in yeast pre-mRNA splicing. In addition, the packing of the bulged RNA helices within the crystal reveals a novel RNA tertiary interaction in which three RNA helices interact through bulged adenosines in the absence of any divalent metal ions.

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References

Qin P, Pyle A . The architectural organization and mechanistic function of group II intron structural elements. Curr Opin Struct Biol. 1998; 8(3):301-8. DOI: 10.1016/s0959-440x(98)80062-6. View

Berglund J, Chua K, Abovich N, REED R, Rosbash M . The splicing factor BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC. Cell. 1997; 89(5):781-7. DOI: 10.1016/s0092-8674(00)80261-5. View

Cowtan K, Main P . Miscellaneous algorithms for density modification. Acta Crystallogr D Biol Crystallogr. 1998; 54(Pt 4):487-93. DOI: 10.1107/s0907444997011980. View

Brunger A, Adams P, Clore G, DeLano W, Gros P, Grosse-Kunstleve R . Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998; 54(Pt 5):905-21. DOI: 10.1107/s0907444998003254. View

Perrotta A, Nikiforova O, Been M . A conserved bulged adenosine in a peripheral duplex of the antigenomic HDV self-cleaving RNA reduceskinetic trapping of inactive conformations. Nucleic Acids Res. 1999; 27(3):795-802. PMC: 148249. DOI: 10.1093/nar/27.3.795. View

Spingola M, Grate L, Haussler D, Ares Jr M . Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. RNA. 1999; 5(2):221-34. PMC: 1369754. DOI: 10.1017/s1355838299981682. View

Podar M, Perlman P . Photocrosslinking of 4-thio uracil-containing RNAs supports a side-by-side arrangement of domains 5 and 6 of a group II intron. RNA. 1999; 5(2):318-29. PMC: 1369762. DOI: 10.1017/s1355838299981724. View

Su L, Chen L, Egli M, Berger J, Rich A . Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot. Nat Struct Biol. 1999; 6(3):285-92. PMC: 7097825. DOI: 10.1038/6722. View

Rutz B, Seraphin B . Transient interaction of BBP/ScSF1 and Mud2 with the splicing machinery affects the kinetics of spliceosome assembly. RNA. 1999; 5(6):819-31. PMC: 1369807. DOI: 10.1017/s1355838299982286. View

10.

Ferre-DAmare A, Doudna J . RNA folds: insights from recent crystal structures. Annu Rev Biophys Biomol Struct. 1999; 28:57-73. DOI: 10.1146/annurev.biophys.28.1.57. View

11.

Ennifar E, Yusupov M, Walter P, Marquet R, Ehresmann B, Ehresmann C . The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges. Structure. 1999; 7(11):1439-49. DOI: 10.1016/s0969-2126(00)80033-7. View

12.

Thiviyanathan V, Guliaev A, Leontis N, Gorenstein D . Solution conformation of a bulged adenosine base in an RNA duplex by relaxation matrix refinement. J Mol Biol. 2000; 300(5):1143-54. DOI: 10.1006/jmbi.2000.3931. View

13.

Arnott S, Hukins D, Dover S, Fuller W, Hodgson A . Structures of synthetic polynucleotides in the A-RNA and A'-RNA conformations: x-ray diffraction analyses of the molecular conformations of polyadenylic acid--polyuridylic acid and polyinosinic acid--polycytidylic acid. J Mol Biol. 1973; 81(2):107-22. DOI: 10.1016/0022-2836(73)90183-6. View

14.

Gutell R, Weiser B, Woese C, Noller H . Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol. 1985; 32:155-216. DOI: 10.1016/s0079-6603(08)60348-7. View

15.

RUSKIN B, Pikielny C, Rosbash M, Green M . Alternative branch points are selected during splicing of a yeast pre-mRNA in mammalian and yeast extracts. Proc Natl Acad Sci U S A. 1986; 83(7):2022-6. PMC: 323222. DOI: 10.1073/pnas.83.7.2022. View

16.

Parker R, Siliciano P, Guthrie C . Recognition of the TACTAAC box during mRNA splicing in yeast involves base pairing to the U2-like snRNA. Cell. 1987; 49(2):229-39. DOI: 10.1016/0092-8674(87)90564-2. View

17.

RUSKIN B, Zamore P, Green M . A factor, U2AF, is required for U2 snRNP binding and splicing complex assembly. Cell. 1988; 52(2):207-19. DOI: 10.1016/0092-8674(88)90509-0. View

18.

Hartmuth K, Barta A . Unusual branch point selection in processing of human growth hormone pre-mRNA. Mol Cell Biol. 1988; 8(5):2011-20. PMC: 363380. DOI: 10.1128/mcb.8.5.2011-2020.1988. View

19.

Adema G, Bovenberg R, Jansz H, Baas P . Unusual branch point selection involved in splicing of the alternatively processed Calcitonin/CGRP-I pre-mRNA. Nucleic Acids Res. 1988; 16(20):9513-26. PMC: 338760. DOI: 10.1093/nar/16.20.9513. View

20.

Zhuang Y, Weiner A . A compensatory base change in human U2 snRNA can suppress a branch site mutation. Genes Dev. 1989; 3(10):1545-52. DOI: 10.1101/gad.3.10.1545. View