Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4.
Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4.
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DOI：
10.1093/nar/gkp158
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发表时间：
2009-05
影响因子：
14.9
通讯作者：
Nureki O
中科院分区：
文献类型：
--
作者：
Suzuki Y;Noma A;Suzuki T;Ishitani R;Nureki O
Wybutosine（yW）是真核生物中最复杂的修饰核苷之一，存在于苯丙氨酸tRNA的反密码子环中。这种高度修饰的核苷通过在核糖体的解码过程中稳定密码子-反密码子配对来确保正确的密码子识别。TYW 4是一种S-腺苷甲硫氨酸（SAM）依赖性酶，催化yW生物合成的最后一步，甲基化和甲氧基羰基化。然而，TYW 4催化机理的结构基础，特别是甲氧基羰基化的结构基础，仍然是难以捉摸的。在这里，我们报告的载脂蛋白和辅因子结合的晶体结构的酵母TYW 4。结构显示C-末端结构域折叠成β-螺旋桨结构，形成靶核苷结合口袋的一部分。TYW 4的载脂蛋白、SAM结合和S-腺苷高半胱氨酸结合结构的比较揭示了辅因子结合后的剧烈结构变化，这可能在反应期间从催化位点螯合溶剂并促进反应后的产物释放。结合功能分析，我们的研究结果表明，TYW 4催化甲基化和甲氧羰基化在一个单一的催化位点，在后者的反应中，甲氧羰基是通过固定二氧化碳形成。
Wybutosine (yW), one of the most complicated modified nucleosides, is found in the anticodon loop of eukaryotic phenylalanine tRNA. This hypermodified nucleoside ensures correct codon recognition by stabilizing codon-anticodon pairings during the decoding process in the ribosome. TYW4 is an S-adenosylmethionine (SAM)-dependent enzyme that catalyzes the final step of yW biosynthesis, methylation and methoxycarbonylation. However, the structural basis for the catalytic mechanism by TYW4, and especially that for the methoxycarbonylation, have remained elusive. Here we report the apo and cofactor-bound crystal structures of yeast TYW4. The structures revealed that the C-terminal domain folds into a β-propeller structure, forming part of the binding pocket for the target nucleoside. A comparison of the apo, SAM-bound, and S-adenosylhomocysteine-bound structures of TYW4 revealed a drastic structural change upon cofactor binding, which may sequester solvent from the catalytic site during the reaction and facilitate product release after the reaction. In conjunction with the functional analysis, our results suggest that TYW4 catalyzes both methylation and methoxycarbonylation at a single catalytic site, and in the latter reaction, the methoxycarbonyl group is formed through the fixation of carbon dioxide.
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DOI：
10.1107/s0907444907040668
发表时间：
2007-10-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Goto-Ito, Sakurako;Ishii, Ryohei;Yokoyama, Shigeyuki
通讯作者：
Yokoyama, Shigeyuki
影响因子：
4.5
作者：
Konevega, AL;Soboleva, NG;Katunin, VI
通讯作者：
Katunin, VI
影响因子：
4.8
作者：
Leulliot, N;Quevillon-Cheruel, S;van Tilbeurgh, H
通讯作者：
van Tilbeurgh, H
影响因子：
16
作者：
Padmanabhan, B;Tong, KI;Yamamoto, M
通讯作者：
Yamamoto, M
影响因子：
64.5
作者：
Ishitani, R;Nureki, O;Yokoyama, S
通讯作者：
Yokoyama, S