Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis
Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis
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DOI：
10.1107/s0907444907040668
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发表时间：
2007-10-01
期刊：
影响因子：
--
通讯作者：
Yokoyama, Shigeyuki
中科院分区：
文献类型：
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作者：
Goto-Ito, Sakurako;Ishii, Ryohei;Yokoyama, Shigeyuki
Wye碱基是在古细菌和真核生物trna中发现的三环碱基。最受修饰的wye碱基，wybutoine，出现在第37位（反密码子的第30个相邻位置），已知对翻译阅读框的维持很重要。酿酒酵母TYW1在酵母碱生物合成中催化三环形成步骤，底物tRNA携带n -1甲基化的G37。本文以2.2埃的分辨率报道了来自堀井焦球菌的古细菌TYW1同源物的晶体结构。P. horikoshii TYW1的氨基酸序列表明它是一种自由基- adomet酶，其三级结构确实具有其他自由基- adomet酶的修饰TIM-barrel结构。Radical-AdoMet酶通常含有一个或两个铁硫（FeS）簇。P. horikoshii TYW1的三级结构显示两个FeS簇位点，每个位点含有三个半胱氨酸残基。一个FeS簇位点预计来自氨基酸序列，另一个涉及分散在整个序列中的半胱氨酸残基。反常傅立叶电子密度图证实了两个FeS团簇的存在。通过将P. horikoshii TYW1的三级结构与其他自由基AdoMet酶的三级结构叠加，在P. horikoshii TYW1中模拟了自由基AdoMet酶反应所必需的AdoMet分子。守恒率和静电电位的表面图显示了高度保守和带正电荷的活性位点空心。基于表面性质，构建了P. horikoshii TYW1与tRNA、FeS簇和AdoMet分子的对接模型，其中tRNA的37位核苷从标准tRNA结构中翻转出来。
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 30-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 angstrom 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.