2yx0

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spinqualitylabelsall models 2yx0, resolution 2.21Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Crystal structure of P. horikoshii TYW1

Overview

Wye bases are tricyclic bases that are found in archaeal and eukaryotic, tRNAs. The most modified wye base, wybutosine, which appears at position, 37 (the 3'-adjacent position to the anticodon), is known to be important, for translational reading-frame maintenance. Saccharomyces cerevisiae TYW1, catalyzes the tri-ring-formation step in wye-base biosynthesis, with the, substrate tRNA bearing N(1)-methylated G37. Here, the crystal structure of, the archaeal TYW1 homologue from Pyrococcus horikoshii is reported at 2.2, A resolution. The amino-acid sequence of P. horikoshii TYW1 suggested that, it is a radical-AdoMet enzyme and the tertiary structure of P. horikoshii, TYW1 indeed shares the modified TIM-barrel structure found in other, radical-AdoMet enzymes. Radical-AdoMet enzymes generally contain one or, two iron-sulfur (FeS) clusters. The tertiary structure of P. horikoshii, TYW1 revealed two FeS cluster sites, each containing three cysteine, residues. One FeS cluster site was expected from the amino-acid sequence, and the other involves cysteine residues that are dispersed throughout the, sequence. The existence of two FeS clusters was confirmed from the, anomalous Fourier electron-density map. By superposing the P. horikoshii, TYW1 tertiary structure on those of other radical-AdoMet enzymes, the, AdoMet molecule, which is necessary for the reactions of radical-AdoMet, enzymes, was modelled in P. horikoshii TYW1. Surface plots of conservation, rates and electrostatic potentials revealed the highly conserved and, positively charged active-site hollow. On the basis of the surface, properties, a docking model of P. horikoshii TYW1, the tRNA, the FeS, clusters and the AdoMet molecule was constructed, with the nucleoside at, position 37 of tRNA flipped out from the canonical tRNA structure.

About this Structure

2YX0 is a Single protein structure of sequence from Pyrococcus horikoshii. Full crystallographic information is available from OCA.

Reference

Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis., Goto-Ito S, Ishii R, Ito T, Shibata R, Fusatomi E, Sekine SI, Bessho Y, Yokoyama S, Acta Crystallogr D Biol Crystallogr. 2007 Oct;63(Pt 10):1059-68. Epub 2007, Sep 19. PMID:17881823

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