Abstract
The atomic coordinates of yeast tRNA(Phe) in the monoclinic crystal form have been determined by an independent analysis from a model built into a 3 A MIR map. The overall molecular structure is found to be in agreement with those reported for the same crystal form by Ladner et al. (1975) and for the orthorhombic form by Quigley et al. (1975) and Kim et al. (1975). However, significant differences between any two of the four models are found in certain local regions of the molecule. The structure is analyzed in terms of the nucleotide stereochemistry and internucleotide phosphodiesters. A striking observation is that the majority of the nucleotide moieties occur in the conformation preferred by the constituent mononucleotides themselves. The internucleotide P-O bonds afford the primary source of flexibility for the folding of the polynucleotide backbone while the sugar pucker and C(4')-C(5') torsions provide the secondary source of flexibility.
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Selected References
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- Altona C., Sundaralingam M. Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation. J Am Chem Soc. 1972 Nov 15;94(23):8205–8212. doi: 10.1021/ja00778a043. [DOI] [PubMed] [Google Scholar]
- Ichikawa T., Sundaralingam M. X-ray diffraction study of a new crystal form of yeast phenylalanine tRNA. Nat New Biol. 1972 Apr 12;236(67):174–175. doi: 10.1038/newbio236174a0. [DOI] [PubMed] [Google Scholar]
- Kim S. H., Suddath F. L., Quigley G. J., McPherson A., Sussman J. L., Wang A. H., Seeman N. C., Rich A. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science. 1974 Aug 2;185(4149):435–440. doi: 10.1126/science.185.4149.435. [DOI] [PubMed] [Google Scholar]
- Ladner J. E., Jack A., Robertus J. D., Brown R. S., Rhodes D., Clark B. F., Klug A. Atomic co-ordinates for yeast phenylalanine tRNA. Nucleic Acids Res. 1975 Sep;2(9):1629–1637. doi: 10.1093/nar/2.9.1629. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ladner J. E., Jack A., Robertus J. D., Brown R. S., Rhodes D., Clark B. F., Klug A. Structure of yeast phenylalanine transfer RNA at 2.5 A resolution. Proc Natl Acad Sci U S A. 1975 Nov;72(11):4414–4418. doi: 10.1073/pnas.72.11.4414. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Prusiner P., Brennan T., Sundaralingam M. Crystal structure and molecular conformation of formycin monohydrates. Possible origin of the anomalous circular dichroic spectra in formycin mono- and polynucleotides. Biochemistry. 1973 Mar 13;12(6):1196–1202. doi: 10.1021/bi00730a028. [DOI] [PubMed] [Google Scholar]
- Quigley G. J., Seeman N. C., Wang A. H., Suddath F. L., Rich A. Yeast phenylalanine transfer RNA: atomic coordinates and torsion angles. Nucleic Acids Res. 1975 Dec;2(12):2329–2341. doi: 10.1093/nar/2.12.2329. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Richards F. M. The matching of physical models to three-dimensional electron-density maps: a simple optical device. J Mol Biol. 1968 Oct 14;37(1):225–230. doi: 10.1016/0022-2836(68)90085-5. [DOI] [PubMed] [Google Scholar]
- Robertus J. D., Ladner J. E., Finch J. T., Rhodes D., Brown R. S., Clark B. F., Klug A. Structure of yeast phenylalanine tRNA at 3 A resolution. Nature. 1974 Aug 16;250(467):546–551. doi: 10.1038/250546a0. [DOI] [PubMed] [Google Scholar]
- Sussman J. L., Kim S. H. Idealized atomic coordinates of yeast phenylalanine transfer RNA. Biochem Biophys Res Commun. 1976 Jan 12;68(1):89–96. doi: 10.1016/0006-291x(76)90014-0. [DOI] [PubMed] [Google Scholar]