8K07

Pseudouridine 5'-monophosphate glycosylase from Arabidopsis thaliana -- citrate bound K185A mutant

8K07 の概要

• エントリーDOI: 10.2210/pdb8k07/pdb
• 分子名称: Pseudouridine-5'-phosphate glycosidase, MANGANESE (II) ION, CITRIC ACID, ... (4 entities in total)
• 機能のキーワード: metalloenzyme, glycosylase, c-nucleoside, pseudouridine monophosphate, metal binding protein, hydrolase
• 由来する生物種: Arabidopsis thaliana (thale cress)
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 109113.15

構造登録者

Lee, J.Y.,Kim, S.H.,Rhee, S.K. (登録日: 2023-07-07, 公開日: 2024-05-15)

主引用文献

Lee, J.,Kim, S.H.,Rhee, S.
Structure and function of the pseudouridine 5'-monophosphate glycosylase PUMY from Arabidopsis thaliana.
Rna Biol., 21:1-10, 2024

PubMed Abstract: Pseudouridine is a noncanonical -nucleoside containing a C-C glycosidic linkage between uracil and ribose. In the two-step degradation of pseudouridine, pseudouridine 5'-monophosphate glycosylase (PUMY) is responsible for the second step and catalyses the cleavage of the C-C glycosidic bond in pseudouridine 5'-monophosphate (ΨMP) into uridine and ribose 5'-phosphate, which are recycled via other metabolic pathways. Structural features of PUMY have been reported, but the details of the substrate specificity of ΨMP were unknown. Here, we present three crystal structures of PUMY in different ligation states and a kinetic analysis of ΨMP degradation. The results indicate that Thr149 and Asn308, which are conserved in the PUMY family, are structural determinants for recognizing the nucleobase of ΨMP. The distinct binding modes of ΨMP and ribose 5'-phosphate also suggest that the nucleobase, rather than the phosphate group, of ΨMP dictates the substrate-binding mode. An open-to-close transition of the active site is essential for catalysis, which is mediated by two α-helices, α11 and α12, near the active site. Mutational analysis validates the proposed roles of the active site residues in catalysis. Our structural and functional analyses provide further insight into the enzymatic features of PUMY towards ΨMP.

PubMed: 38117089
DOI: 10.1080/15476286.2023.2293340

実験手法

X-RAY DIFFRACTION (1.121 Å)