4RDI

Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA

4RDI の概要

• エントリーDOI: 10.2210/pdb4rdi/pdb
• 関連するPDBエントリー: 4RDH
• 分子名称: tRNA threonylcarbamoyladenosine dehydratase, ADENOSINE-5'-TRIPHOSPHATE, GLYCEROL, ... (4 entities in total)
• 機能のキーワード: rossmann fold, dehydratase, ligase
• 由来する生物種: Escherichia coli
• 細胞内の位置: Membrane ; Single-pass membrane protein : Q46927
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 127342.39

構造登録者

Park, S.Y.,Kim, S.,Lee, H. (登録日: 2014-09-19, 公開日: 2015-08-05, 最終更新日: 2024-10-16)

主引用文献

Kim, S.,Lee, H.,Park, S.
The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N(6)-Threonylcarbamoyladenosine Dehydratase Activity.
J.Mol.Biol., 427:3074-3085, 2015

PubMed Abstract: Escherichia coli TcdA (also known as CsdL) was previously shown to catalyze the ATP-dependent dehydration/cyclization of hypermodified tRNA N(6)-threonylcarbamoyladenosine into further cyclic N(6)-threonylcarbamoyladenosine. In this study, we report the X-ray crystal structures of E. coli TcdA with either AMP or ATP bound. The AMP/ATP-bound N-terminal sub-domain of TcdA resembles the ATP-binding Rossmann fold of E. coli ThiF and MoeB that are enzymes respectively taking part in the biosynthesis of thiamine and molybdopterin; however, the remaining C-terminal sub-domain of TcdA adopts a structure unrelated to any other known folds. In TcdA, the ATP-utilizing adenylation of tRNA N(6)-threonylcarbamoyladenosine and a subsequent thioester formation via an active cysteine, similar to the mechanisms in ThiF and MoeB, could take place for the dehydratase function. Analysis of the structure with sequence alignment suggests the disordered Cys234 of TcdA as the most likely catalytic residue. The structure further indicates that the C-terminal sub-domain can provide a binding interface for the tRNA substrate. Binding study using the surface mutants of TcdA and tRNA reveals that the positively charged regions of mainly the C-terminal sub-domain are important for the tRNA recognition.

PubMed: 26101842
DOI: 10.1016/j.jmb.2015.06.005

実験手法

X-RAY DIFFRACTION (1.95 Å)