2ZXI

Structure of Aquifex aeolicus GidA in the form II crystal

2ZXI の概要

• エントリーDOI: 10.2210/pdb2zxi/pdb
• 関連するPDBエントリー: 2ZXH
• 分子名称: tRNA uridine 5-carboxymethylaminomethyl modification enzyme mnmG, FLAVIN-ADENINE DINUCLEOTIDE (3 entities in total)
• 機能のキーワード: modification, trna, 5-carboxymethylaminomethyl uridine, wobble uridine, fad, fad-binding protein, trna modification enzyme
• 由来する生物種: Aquifex aeolicus
• 細胞内の位置: Cytoplasm (By similarity): O66962
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 290439.42

構造登録者

Numata, T.,Osawa, T. (登録日: 2008-12-24, 公開日: 2009-05-19, 最終更新日: 2023-11-01)

主引用文献

Osawa, T.,Ito, K.,Inanaga, H.,Nureki, O.,Tomita, K.,Numata, T.
Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon
Structure, 17:713-724, 2009

PubMed Abstract: The 5-carboxymethylaminomethyl modification of uridine (cmnm(5)U) at the anticodon first position occurs in tRNAs that read split codon boxes ending with purine. This modification is crucial for correct translation, by restricting codon-anticodon wobbling. Two conserved enzymes, GidA and MnmE, participate in the cmnm(5)U modification process. Here we determined the crystal structure of Aquifex aeolicus GidA at 2.3 A resolution. The structure revealed the tight interaction of GidA with FAD. Structure-based mutation analyses allowed us to identify two conserved Cys residues in the vicinity of the FAD-binding site that are essential for the cmnm(5)U modification in vivo. Together with mutational analysis of MnmE, we propose a mechanism for the cmnm(5)U modification process where GidA, but not MnmE, attacks the C6 atom of uridine by a mechanism analogous to that of thymidylate synthase. We also present a tRNA-docking model that provides structural insights into the tRNA recognition mechanism for efficient modification.

PubMed: 19446527
DOI: 10.1016/j.str.2009.03.013

実験手法

X-RAY DIFFRACTION (2.3 Å)