Anticodon-anticodon Interaction Induces Conformational Changes in TRNA: Yeast TRNAAsp, a Model for TRNA-mRNA Recognition

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1986 Feb 1

PMID 3513167

Citations 18

Authors

D Moras

A C Dock

P Dumas

E Westhof

P Romby

J P Ebel

R Giege

Affiliations

Soon will be listed here.

Abstract

The crystal structure of yeast tRNAAsp enables visualization of an anticodon-anticodon interaction at the molecular level. Except for differences in the base stacking and twist, the overall conformation of the anticodon loop is quite similar to that of yeast tRNAPhe. The anticodon nucleotide triplets, GUC, of two symmetrically related molecules form a minihelix of the RNA type 11. The modified base m1G37 stacks on both sides of the triplets and enforces the continuity with the anticodon stems. Anticodon association induces long-range conformational changes in the region of the dihydrouracil and thymine loops. Experimental evidence includes the variation in the distribution of temperature factors between yeast tRNAPhe and tRNAAsp, the difference in the self-splitting patterns of tRNAAsp in crystal and solution, and the differential accessibility of cytidines to dimethyl sulfate in free and duplex tRNAAsp. These observations are linked to the fragility and disruption of the G.C Watson-Crick base pair at the corner of the molecule formed by the dihydrouracil and thymine loops.

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References

QUIGLEY G, Teeter M, Rich A . Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA. Proc Natl Acad Sci U S A. 1978; 75(1):64-8. PMC: 411184. DOI: 10.1073/pnas.75.1.64. View

Rubin J, Sundaralingam M . Lead ion binding and RNA chain hydrolysis in phenylalanine tRNA. J Biomol Struct Dyn. 1983; 1(3):639-46. DOI: 10.1080/07391102.1983.10507471. View

Grosjean H, de Henau S, Crothers D . On the physical basis for ambiguity in genetic coding interactions. Proc Natl Acad Sci U S A. 1978; 75(2):610-4. PMC: 411305. DOI: 10.1073/pnas.75.2.610. View

Sussman J, Holbrook S, Warrant R, Church G, Kim S . Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement. J Mol Biol. 1978; 123(4):607-30. DOI: 10.1016/0022-2836(78)90209-7. View

Bruce A, Uhlenbeck O . Reactions at the termini of tRNA with T4 RNA ligase. Nucleic Acids Res. 1978; 5(10):3665-77. PMC: 342702. DOI: 10.1093/nar/5.10.3665. View

Schevitz R, Podjarny A, Krishnamachari N, Hughes J, SIGLER P, Sussman J . Crystal structure of a eukaryotic initiator tRNA. Nature. 1979; 278(5700):188-90. DOI: 10.1038/278188a0. View

Davanloo P, Sprinzl M, Cramer F . Proton nuclear magnetic resonance of minor nucleosides in yeast phenylalanine transfer ribonucleic acid. Conformational changes as a consequence of aminoacylation, removal of the Y base, and codon--anticodon interaction. Biochemistry. 1979; 18(15):3189-99. DOI: 10.1021/bi00582a001. View

Wagner R, Garrett R . Chemical evidence for a codon-induced allosteric change in tRNALys involving the 7-methylguanosine residue 46. Eur J Biochem. 1979; 97(2):615-21. DOI: 10.1111/j.1432-1033.1979.tb13151.x. View

Yokoyama S, Miyazawa T, Iitaka Y, Yamaizumi Z, Kasai H, Nishimura S . Three-dimensional structure of hyper-modified nucleoside Q located in the wobbling position of tRNA. Nature. 1979; 282(5734):107-9. DOI: 10.1038/282107a0. View

10.

Woo N, Roe B, Rich A . Three-dimensional structure of Escherichia coli initiator tRNAfMet. Nature. 1980; 286(5771):346-51. DOI: 10.1038/286346a0. View

11.

Peattie D, Gilbert W . Chemical probes for higher-order structure in RNA. Proc Natl Acad Sci U S A. 1980; 77(8):4679-82. PMC: 349909. DOI: 10.1073/pnas.77.8.4679. View

12.

Farber N, Cantor C . Comparison of the structures of free and ribosome-bound tRNAPhe by using slow tritium exchange. Proc Natl Acad Sci U S A. 1980; 77(9):5135-9. PMC: 350011. DOI: 10.1073/pnas.77.9.5135. View

13.

Geerdes H, VAN Boom J, Hilbers C . Nuclear magnetic resonance studies of codon-anticodon interaction in tRNAPhe. I. Effect of binding complementary tetra and pentanucleotides to the anticodon. J Mol Biol. 1980; 142(2):195-217. DOI: 10.1016/0022-2836(80)90045-5. View

14.

Grosjean H, CHANTRENNE H . On codon- anticodon interactions. Mol Biol Biochem Biophys. 1980; 32:347-67. DOI: 10.1007/978-3-642-81503-4_27. View

15.

Moras D, Comarmond M, Fischer J, Weiss R, Thierry J, Ebel J . Crystal structure of yeast tRNAAsp. Nature. 1980; 288(5792):669-74. DOI: 10.1038/288669a0. View

16.

GASSEN H . Ligand-induced conformational changes in ribonucleic acids. Prog Nucleic Acid Res Mol Biol. 1980; 24:57-86. DOI: 10.1016/s0079-6603(08)60671-6. View

17.

Pace B, Matthews E, Johnson K, Cantor C, Pace N . Conserved 5S rRNA complement to tRNA is not required for protein synthesis. Proc Natl Acad Sci U S A. 1982; 79(1):36-40. PMC: 345656. DOI: 10.1073/pnas.79.1.36. View

18.

Boutorin A, Clark B, Ebel J, Kruse T, Petersen H, Remy P . A study of the interaction of Escherichia coli elongation factor-Tu with aminoacyl-tRNAs by partial digestion with cobra venom ribonuclease. J Mol Biol. 1981; 152(3):593-608. DOI: 10.1016/0022-2836(81)90271-0. View

19.

Vlassov V, Giege R, Ebel J . Tertiary structure of tRNAs in solution monitored by phosphodiester modification with ethylnitrosourea. Eur J Biochem. 1981; 119(1):51-9. DOI: 10.1111/j.1432-1033.1981.tb05575.x. View

20.

Yarus M . Translational efficiency of transfer RNA's: uses of an extended anticodon. Science. 1982; 218(4573):646-52. DOI: 10.1126/science.6753149. View