Literature DB >> 10943889

The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited.

H Shi1, P B Moore.   

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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Year:  2000        PMID: 10943889      PMCID: PMC1369984          DOI: 10.1017/s1355838200000364

Source DB:  PubMed          Journal:  RNA        ISSN: 1355-8382            Impact factor:   4.942


  23 in total

1.  RNA hydration: a detailed look.

Authors:  M Egli; S Portmann; N Usman
Journal:  Biochemistry       Date:  1996-07-02       Impact factor: 3.162

2.  Atomic coordinates and molecular conformation of yeast phenylalanyl tRNA. An independent investigation.

Authors:  C D Stout; H Mizuno; J Rubin; T Brennan; S T Rao; M Sundaralingam
Journal:  Nucleic Acids Res       Date:  1976-04       Impact factor: 16.971

3.  Further refinement of the structure of yeast tRNAPhe.

Authors:  B Hingerty; R S Brown; A Jack
Journal:  J Mol Biol       Date:  1978-09-25       Impact factor: 5.469

4.  Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement.

Authors:  J L Sussman; S R Holbrook; R W Warrant; G M Church; S H Kim
Journal:  J Mol Biol       Date:  1978-08-25       Impact factor: 5.469

5.  A crystallographic study of metal-binding to yeast phenylalanine transfer RNA.

Authors:  A Jack; J E Ladner; D Rhodes; R S Brown; A Klug
Journal:  J Mol Biol       Date:  1977-04-15       Impact factor: 5.469

6.  Three-dimensional tertiary structure of yeast phenylalanine transfer RNA.

Authors:  S H Kim; F L Suddath; G J Quigley; A McPherson; J L Sussman; A H Wang; N C Seeman; A Rich
Journal:  Science       Date:  1974-08-02       Impact factor: 47.728

7.  X-ray crystallographic studies of polymorphic forms of yeast phenylalanine transfer RNA.

Authors:  S H Kim; G Quigley; F L Suddath; A McPherson; D Sneden; J J Kim; J Weinzierl; A Rich
Journal:  J Mol Biol       Date:  1973-04-05       Impact factor: 5.469

8.  Crystal and molecular structure of r(CGCGAAUUAGCG): an RNA duplex containing two G(anti).A(anti) base pairs.

Authors:  G A Leonard; K E McAuley-Hecht; S Ebel; D M Lough; T Brown; W N Hunter
Journal:  Structure       Date:  1994-06-15       Impact factor: 5.006

9.  Three-dimensional structure of a hammerhead ribozyme.

Authors:  H W Pley; K M Flaherty; D B McKay
Journal:  Nature       Date:  1994-11-03       Impact factor: 49.962

10.  Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement.

Authors:  L M Rice; A T Brünger
Journal:  Proteins       Date:  1994-08
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  178 in total

1.  Calculation of hydrodynamic properties of small nucleic acids from their atomic structure.

Authors:  M X Fernandes; A Ortega; M C López Martínez; J García de la Torre
Journal:  Nucleic Acids Res       Date:  2002-04-15       Impact factor: 16.971

2.  Effects of magnesium ions on the stabilization of RNA oligomers of defined structures.

Authors:  Martin J Serra; John D Baird; Taraka Dale; Bridget L Fey; Kimberly Retatagos; Eric Westhof
Journal:  RNA       Date:  2002-03       Impact factor: 4.942

3.  A critical role of water in the specific cleavage of the anticodon loop of some eukaryotic methionine initiator tRNAs.

Authors:  Marcus Perbandt; Miroslawa Z Barciszewska; Christian Betzel; Volker A Erdmann; Jan Barciszewski
Journal:  Mol Biol Rep       Date:  2003-03       Impact factor: 2.316

4.  Site-specific platinum(II) cross-linking in a ribozyme active site.

Authors:  Erich G Chapman; Victoria J DeRose
Journal:  J Am Chem Soc       Date:  2011-12-14       Impact factor: 15.419

5.  Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit.

Authors:  Hu Pan; Sanjay Agarwalla; Demetri T Moustakas; Janet Finer-Moore; Robert M Stroud
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-17       Impact factor: 11.205

6.  The rate-limiting step in the folding of a large ribozyme without kinetic traps.

Authors:  X-W Fang; P Thiyagarajan; T R Sosnick; T Pan
Journal:  Proc Natl Acad Sci U S A       Date:  2002-06-25       Impact factor: 11.205

7.  On the occurrence of the T-loop RNA folding motif in large RNA molecules.

Authors:  Andrey S Krasilnikov; Alfonso Mondragón
Journal:  RNA       Date:  2003-06       Impact factor: 4.942

8.  Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs.

Authors:  Uma Nagaswamy; George E Fox
Journal:  RNA       Date:  2002-09       Impact factor: 4.942

9.  Specific phosphorothioate substitutions probe the active site of Bacillus subtilis ribonuclease P.

Authors:  Sharon M Crary; Jeffrey C Kurz; Carol A Fierke
Journal:  RNA       Date:  2002-07       Impact factor: 4.942

10.  Purine bases at position 37 of tRNA stabilize codon-anticodon interaction in the ribosomal A site by stacking and Mg2+-dependent interactions.

Authors:  Andrey L Konevega; Natalia G Soboleva; Valentin I Makhno; Yuri P Semenkov; Wolfgang Wintermeyer; Marina V Rodnina; Vladimir I Katunin
Journal:  RNA       Date:  2004-01       Impact factor: 4.942

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