4tra

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RESTRAINED REFINEMENT OF TWO CRYSTALLINE FORMS OF YEAST ASPARTIC ACID AND PHENYLALANINE TRANSFER RNA CRYSTALS

Overview

Four transfer RNA crystals, the monoclinic and orthorhombic forms of yeast, tRNA(Phe) as well as forms A and B of yeast tRNA(Asp), have been submitted, to the same restrained least-squares refinement program and refined to an, R factor well below 20% for about 4500 reflections between 10 and 3 A. In, yeast tRNA(Asp) crystals the molecules exist as dimers with base pairings, of the anticodon (AC) triplets and labilization of the tertiary, interaction between one invariant guanine of the dihydrouridine (D) loop, and the invariant cytosine of the thymine (T) loop (G19-C56). In yeast, tRNA(Phe) crystals, the molecules exist as monomers with only weak, intermolecular packing contacts between symmetry-related molecules., Despite this, the tertiary folds of the L-shaped tRNA structures are, identical when allowance is made for base sequence changes between, tRNA(Phe) and tRNA(Asp). However, the relative mobilities of two regions, are inverse in the two structures with the AC loop more mobile than the D, loop in tRNA(Phe) and the D loop more mobile than the AC loop in, tRNA(Asp). In addition, the T loop becomes mobile in tRNA(Asp). The, present refinements were performed to exclude packing effects or, refinement bias as possible sources of such differential dynamic behavior., It is concluded that the transfer of flexibility from the anticodon to the, D- and T-loop region in tRNA(Asp) is not a crystal-line artefact. Further, analysis of the four structures supports a mechanism for the flexibility, transfer through base stacking in the AC loop and concomitant variations, in twist angles between base pairs of the anticodon helix which propagate, up to the D- and T-loop region.

About this Structure

4TRA is a Protein complex structure of sequences from Saccharomyces cerevisiae with MG as ligand. Full crystallographic information is available from OCA.

Reference

Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals., Westhof E, Dumas P, Moras D, Acta Crystallogr A. 1988 Mar 1;44 ( Pt 2):112-23. PMID:3272146

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