6AGG

Crystal structure of agmatine-AMPPCP-Mg complexed TiaS (tRNAIle2 agmatidine synthetase)

6AGG の概要

• エントリーDOI: 10.2210/pdb6agg/pdb
• 関連するPDBエントリー: 5XOB
• 分子名称: tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS, ZINC ION, PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER, ... (8 entities in total)
• 機能のキーワード: zinc ribbon, conformational change, tias, trna modification, zinc finger engineering, ligase
• 由来する生物種: Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 49257.98

構造登録者

Dong, J.S.,Gong, W.M. (登録日: 2018-08-11, 公開日: 2018-09-05, 最終更新日: 2024-10-23)

主引用文献

Dong, J.,Li, F.,Gao, F.,Wei, J.,Lin, Y.,Zhang, Y.,Lou, J.,Liu, G.,Dong, Y.,Liu, L.,Liu, H.,Wang, J.,Gong, W.
Structure of tRNA-Modifying Enzyme TiaS and Motions of Its Substrate Binding Zinc Ribbon.
J. Mol. Biol., 430:4183-4194, 2018

PubMed Abstract: The accurate modification of the tRNA anticodon wobble cytosine 34 is critical for AUA decoding in protein synthesis. Archaeal tRNA cytosine 34 is modified with agmatine in the presence of ATP by TiaS (tRNA agmatidine synthetase). However, no structure of apo-form full-length TiaS is available currently. Here, the crystal structures of apo TiaS and a complex of TiaS-agmatine-AMPPCP-Mg are presented, with properly folded zinc ribbon and Cys4-zinc coordination identified. Compared with tRNA-bound form, the architecture of apo TiaS shows a totally different conformation of zinc ribbon. Molecular dynamics simulations of the docking complex between free-state TiaS and tRNA suggest that zinc ribbon domain is capable of performing large-scale motions to sample substrate binding-competent conformation. Principle component analysis and normal mode analysis show consistent results about the relative directionality of functionally correlated zinc ribbon motions. Apo TiaS and TiaS-agmatine-AMPPCP-Mg/TiaS-AMPCPP-Mg complex structures capture two snapshots of the flexible ATP-Mg binding p2loop step-by-step stabilization. Research from this study provides new insight into TiaS functional mechanism and the dynamic feature of zinc ribbons.

PubMed: 30121296
DOI: 10.1016/j.jmb.2018.08.015

実験手法

X-RAY DIFFRACTION (2.706 Å)