Three-Dimensional Structure of Yeast Phenylalanine Transfer RNA: Folding of the Polynucleotide Chain

@article{Kim1973ThreeDimensionalSO,
  title={Three-Dimensional Structure of Yeast Phenylalanine Transfer RNA: Folding of the Polynucleotide Chain},
  author={Sun Hwa Kim and G. J. Quigley and Fred Leroy Suddath and Alexander McPherson and D. Sneden and Jenny J. Kim and Jon E. Weinzierl and Alexander Rich},
  journal={Science},
  year={1973},
  volume={179},
  pages={285 - 288}
}
At 4 � resolution the polynucleotides in yeast phenylalanine transfer RNA are seen in a series of electron dense masses about 5.8 � apart. These peaks are probably associated with the phosphate groups, while lower levels of electron density between segments of adjacent polynucleotide chains are interpreted as arising from hydrogen-bonded purine-pyrimidine base pairs. It is possible to trace the entire polynucleotide chain with only two minor regions of ambiguity. The polynucleotide chain has a… 
Three-Dimensional Tertiary Structure of Yeast Phenylalanine Transfer RNA
TLDR
The 3-angstrom electron density map of crystalline yeast phenylalanine transfer RNA has provided us with a complete three-dimensional model which defines the positions of all of the nucleotide residues in the moleclule, which explains, in a simple and direct fashion, chemical modification studies of transfer RNA.
Orientation of double-helical segments in crystals of yeast phenylalanine transfer RNA.
  • M. Levitt
  • Chemistry, Medicine
    Journal of molecular biology
  • 1973
TLDR
A search of the X-ray intensities of the P 2 1 crystal form of yeast transfer RNA Phe has revealed the orientation of the double-helical segments in the crystal, revealing a “boot”-shaped molecule, which may be derived from an earlier model proposed by the author, by bending out the anticodon arm.
Crystal structure of yeast phenylalanine transfer RNA. II. Structural features and functional implications.
TLDR
The structural features of yeast phenylalanine transfer RNA are analyzed and documented in detail, based on atomic co-ordinates obtained from an extensive crystallographic refinement of the crystal structure of the molecule at 2.7 A resolution, finding a considerable irregularity in the helicity of the base-paired stems, a greater flexibility in the anticodon and aminoacyl acceptor arms, and a “coupling” among several conformational angles.
Structural domains of transfer RNA molecules.
TLDR
Various detailed features of the conformation of yeast tRNA(Phe) revealed by recent refinement analysis of x-ray diffraction data at 2.5 A resolution are described.
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The structure indicates the extent of RNA packing required for the function of large ribozymes, the spliceosome, and the ribosome.
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The structure of a 29-nucleotide RNA containing the sarcin/ricin loop (SRL) of rat 28 S rRNA has been determined and comparisons with other RNA crystal structures establish the cross-strand A stack and the GNRA tetraloop as defined and modular RNA structural elements.
A pseudoknotted RNA oligonucleotide
TLDR
Results show that appropriate sequences can form pseudoknots and indicate that pseudok nots are a significant type of local tertiary structure which must be considered in the folding of complex RNA molecules.
Transfer RNA and the translation apparatus in the origin of life
  • A. Rich
  • Biology, Medicine
    Origins of life
  • 2004
TLDR
Comments are made about the manner in which the tRNA molecule may have evolved and in addition, some suggestions are presented about the prebiotic interactions of primitive tRNA polynucleotides and messenger RNA strands.
A conformational rationale for the origin of the mechanism of nucleicacid-directed protein synthesis of ‘living’ organisms
TLDR
The nucleicacid-directed protein synthesis is shown to be a natural consequence of a particular way of favourable interaction between nucleic acids and amino acids, and the model provides the missing link between the chemical evolution of small organic molecules and biological evolution through the process of mutations in nucleicacids and nucleic acid-directedprotein synthesis.
Alternative Tertiary Structure of tRNA for Recognition by a Posttranscriptional Modification Enzyme
TLDR
The crystal structure of tRNA bound with archaeosine tRNA-guanine transglycosylase is determined, which modifies G15 of the D arm in the core of the core, by counting the nucleotide number from G1 to G15 in the lambda form.
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References

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The three-dimensional structure of yeast phenylalanine transfer RNA: shape of the molecule at 5.5-A resolution.
  • S. Kim, G. Quigley, +6 authors A. Rich
  • Chemistry, Medicine
    Proceedings of the National Academy of Sciences of the United States of America
  • 1972
TLDR
Three isomorphous heavy-atom derivatives have been obtained of orthorhombic crystals of phenylalanine transfer RNA from yeast, and the data suggest no apparent similarity between the folding of the molecule and any of the tertiary structure models proposed for transfer RNA.
High-resolution x-ray diffraction patterns of crystalline transfer RNA that show helical regions.
TLDR
From an analysis of the packing in the unit cell it is concluded that the molecular dimensions are approximately 80 by 33 by 28 A, indicating that the double-helical portions of the transfer RNA molecule are approximately half a helical turn in length, and therefore can contain 4-7 base pairs.
Structure of Transfer RNA: Evidence for Interaction between Two Non-adjacent Nucleotide Residues in tRNAVal1 from Escherichia coli
These two letters describe the interaction between two non-adjacent residues in tRNAVal1 at position eight and thirteen, and a new model of the tRNA molecule that takes into account this restriction.
Amino-acid Composition of Crayfish Trypsin
TLDR
The amino-acid composition of trypsinogen isolated from the pancreas of the spiny Pacific dogfish is studied and a preliminary examination of the primary structure of this enzyme is presented, showing a high degree of homology as compared with bovine tryps inogen.
Structure of a Ribonucleic Acid
The complete nucleotide sequence of an alanine transfer RNA, isolated from yeast, has been determined. This is the first nucleic acid for which the structure is known.
If an effect of this type does occur it could be of considerable importance in understanding various mechanisms that exist in charging tRNA
  • Biological and Biochemical Basis of Behavior
NSF, NASA, the American Cancer Society; and by an NIH postdoctoral fellowship to GJ
  • Supported by grants from NIH (CA 04186-15 at M.I.T. and GM 15000-04 at the Biochemistry Department