1Q2S

Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate

1Q2S の概要

• エントリーDOI: 10.2210/pdb1q2s/pdb
• 関連するPDBエントリー: 1Q2R
• 分子名称: 5'-R(*AP*GP*CP*AP*CP*GP*GP*CP*UP*(PQ1)P*UP*AP*AP*AP*CP*CP*GP*UP*GP*C)-3', RNA (5'-R(*AP*GP*CP*AP*CP*GP*GP*CP*UP*(N)P*UP*AP*AP*AP*CP*CP*GP*UP*GP*C)-3'), Queuine tRNA-ribosyltransferase, ... (6 entities in total)
• 機能のキーワード: tim barrel, protein-rna complex, covalent intermediat, transferase-rna complex, transferase/rna
• 由来する生物種: Zymomonas mobilis; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 184837.32

構造登録者

Xie, W.,Liu, X.,Huang, R.H. (登録日: 2003-07-25, 公開日: 2003-09-09, 最終更新日: 2023-08-16)

主引用文献

Xie, W.,Liu, X.,Huang, R.H.
Chemical trapping and crystal structure of a catalytic tRNA guanine transglycosylase covalent intermediate
Nat.Struct.Biol., 10:781-788, 2003

PubMed Abstract: Prokaryotic tRNA guanine transglycosylase (TGT) catalyzes replacement of guanine (G) by 7-aminomethyl-7-deazaguanine (PreQ1) at the wobble position of four specific tRNAs. Addition of 9-deazaguanine (9dzG) to a reaction mixture of Zymomonas mobilis TGT and an RNA substrate allowed us to trap, purify and crystallize a chemically competent covalent intermediate of the TGT-catalyzed reaction. The crystal structure of the TGT-RNA-9dzG ternary complex at a resolution of 2.9 A reveals, unexpectedly, that RNA is tethered to TGT through the side chain of Asp280. Thus, Asp280, instead of the previously proposed Asp102, acts as the nucleophile for the reaction. The RNA substrate adopts an unusual conformation, with four out of seven nucleotides in the loop region flipped out. Interactions between TGT and RNA revealed by the structure provide the molecular basis of the RNA substrate requirements by TGT. Furthermore, reaction of PreQ1 with the crystallized covalent intermediate provides insight into the necessary structural changes required for the TGT-catalyzed reaction to occur.

PubMed: 12949492
DOI: 10.1038/nsb976

実験手法

X-RAY DIFFRACTION (3.2 Å)