4GIM

Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-phosphate

4GIM の概要

• エントリーDOI: 10.2210/pdb4gim/pdb
• 関連するPDBエントリー: 4GIJ 4GIK 4GIL
• 分子名称: Pseudouridine-5'-phosphate glycosidase, PSEUDOURIDINE-5'-MONOPHOSPHATE, MANGANESE (II) ION, ... (4 entities in total)
• 機能のキーワード: alpha-beta-alpha sandwich fold, hydrolase
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 107834.01

構造登録者

Huang, S.,Mahanta, N.,Begley, T.P.,Ealick, S.E. (登録日: 2012-08-08, 公開日: 2012-10-31, 最終更新日: 2023-09-13)

主引用文献

Huang, S.,Mahanta, N.,Begley, T.P.,Ealick, S.E.
Pseudouridine monophosphate glycosidase: a new glycosidase mechanism.
Biochemistry, 51:9245-9255, 2012

PubMed Abstract: Pseudouridine (Ψ), the most abundant modification in RNA, is synthesized in situ using Ψ synthase. Recently, a pathway for the degradation of Ψ was described [Preumont, A., Snoussi, K., Stroobant, V., Collet, J. F., and Van Schaftingen, E. (2008) J. Biol. Chem. 283, 25238-25246]. In this pathway, Ψ is first converted to Ψ 5'-monophosphate (ΨMP) by Ψ kinase and then ΨMP is degraded by ΨMP glycosidase to uracil and ribose 5-phosphate. ΨMP glycosidase is the first example of a mechanistically characterized enzyme that cleaves a C-C glycosidic bond. Here we report X-ray crystal structures of Escherichia coli ΨMP glycosidase and a complex of the K166A mutant with ΨMP. We also report the structures of a ring-opened ribose 5-phosphate adduct and a ring-opened ribose ΨMP adduct. These structures provide four snapshots along the reaction coordinate. The structural studies suggested that the reaction utilizes a Lys166 adduct during catalysis. Biochemical and mass spectrometry data further confirmed the existence of a lysine adduct. We used site-directed mutagenesis combined with kinetic analysis to identify roles for specific active site residues. Together, these data suggest that ΨMP glycosidase catalyzes the cleavage of the C-C glycosidic bond through a novel ribose ring-opening mechanism.

PubMed: 23066817
DOI: 10.1021/bi3006829

実験手法

X-RAY DIFFRACTION (1.802 Å)