The Crystal Structure of Yeast Phenylalanine TRNA at 1.93 A Resolution: a Classic Structure Revisited

Overview

Journal RNA

Specialty Molecular Biology

Date 2000 Aug 16

PMID 10943889

Citations 207

Authors

H Shi

P B Moore

Affiliations

Soon will be listed here.

Abstract

The crystal structure of the monoclinic form of yeast phenylalanine tRNA has been redetermined at a resolution of 1.93 A. The structure of yeast tRNAphe described here is more accurate than its predecessors not only because it incorporates higher resolution data, but also because it has been refined using techniques that had not been developed when its predecessors were determined more than 20 years ago. The 1.93 A resolution version of this structure differs interestingly from its predecessors in its details. In loop regions particularly, the backbone torsion angles in the new structure are not the same as those reported earlier. Several new divalent cation binding sites have been identified, and the water structure that has emerged is also different.

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References

Kim S, Suddath F, QUIGLEY G, McPherson A, Sussman J, Wang A . Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science. 1974; 185(4149):435-40. DOI: 10.1126/science.185.4149.435. View

Kim S, Quigley G, Suddath F, McPherson A, Sneden D, Kim J . X-ray crystallographic studies of polymorphic forms of yeast phenylalanine transfer RNA. J Mol Biol. 1973; 75(2):421-8. DOI: 10.1016/0022-2836(73)90031-4. View

Stout C, Mizuno H, Rubin J, Brennan T, Rao S, Sundaralingam M . Atomic coordinates and molecular conformation of yeast phenylalanyl tRNA. An independent investigation. Nucleic Acids Res. 1976; 3(4):1111-23. PMC: 342970. DOI: 10.1093/nar/3.4.1111. View

Jack A, Ladner J, Rhodes D, Brown R, Klug A . A crystallographic study of metal-binding to yeast phenylalanine transfer RNA. J Mol Biol. 1977; 111(3):315-28. DOI: 10.1016/s0022-2836(77)80054-5. 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

Hingerty B, Brown R, Jack A . Further refinement of the structure of yeast tRNAPhe. J Mol Biol. 1978; 124(3):523-34. DOI: 10.1016/0022-2836(78)90185-7. View

Leonard G, Ebel S, Lough D, Brown T, Hunter W . Crystal and molecular structure of r(CGCGAAUUAGCG): an RNA duplex containing two G(anti).A(anti) base pairs. Structure. 1994; 2(6):483-94. DOI: 10.1016/S0969-2126(00)00049-6. View

Pley H, Flaherty K, McKay D . Three-dimensional structure of a hammerhead ribozyme. Nature. 1994; 372(6501):68-74. DOI: 10.1038/372068a0. View

Rice L, Brunger A . Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins. 1994; 19(4):277-90. DOI: 10.1002/prot.340190403. View

10.

Egli M, Portmann S, Usman N . RNA hydration: a detailed look. Biochemistry. 1996; 35(26):8489-94. DOI: 10.1021/bi9607214. View

11.

Correll C, Freeborn B, Moore P, Steitz T . Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell. 1997; 91(5):705-12. DOI: 10.1016/s0092-8674(00)80457-2. View

12.

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

13.

Correll C, Munishkin A, Chan Y, Ren Z, Wool I, Steitz T . Crystal structure of the ribosomal RNA domain essential for binding elongation factors. Proc Natl Acad Sci U S A. 1998; 95(23):13436-41. PMC: 24837. DOI: 10.1073/pnas.95.23.13436. View

14.

Rubin J, Wang J, Sundaralingam M . X-ray diffraction study of the zinc(II) binding sites in yeast phenylalanine transfer RNA. Preferential binding of zinc to guanines in purine-purine sequences. Biochim Biophys Acta. 1983; 756(1):111-8. DOI: 10.1016/0304-4165(83)90030-2. View

15.

Westhof E, Sundaralingam M . Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles. Biochemistry. 1986; 25(17):4868-78. DOI: 10.1021/bi00365a022. View

16.

Saenger W, Hunter W, KENNARD O . DNA conformation is determined by economics in the hydration of phosphate groups. Nature. 1986; 324(6095):385-8. DOI: 10.1038/324385a0. View

17.

Keith G, DIRHEIMER G . Evidence for the existence of an expressed minor variant tRNAPhe in yeast. Biochem Biophys Res Commun. 1987; 142(1):183-7. DOI: 10.1016/0006-291x(87)90468-2. View

18.

KENNARD O, Cruse W, Nachman J, Prange T, Shakked Z, Rabinovich D . Ordered water structure in an A-DNA octamer at 1.7 A resolution. J Biomol Struct Dyn. 1986; 3(4):623-47. DOI: 10.1080/07391102.1986.10508452. View

19.

Westhof E, Dumas P, Moras D . Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals. Acta Crystallogr A. 1988; 44 ( Pt 2):112-23. View

20.

Brunger A, Krukowski A, Erickson J . Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallogr A. 1990; 46 ( Pt 7):585-93. DOI: 10.1107/s0108767390002355. View