7VSK

Crystal structure of E.coli pseudouridine kinase PsuK complexed with pseudouridine.

7VSK の概要

• エントリーDOI: 10.2210/pdb7vsk/pdb
• 分子名称: PfkB domain protein, 5-[(2~{S},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1~{H}-pyrimidine-2,4-dione (3 entities in total)
• 機能のキーワード: pseudouridine, kinase, yeic, rna binding protein
• 由来する生物種: Escherichia coli (strain B / BL21-DE3)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 34025.29

構造登録者

Li, K.J.,Li, X.J.,Wu, B.X. (登録日: 2021-10-26, 公開日: 2022-06-22, 最終更新日: 2023-11-29)

主引用文献

Li, X.,Li, K.,Guo, W.,Wen, Y.,Meng, C.,Wu, B.
Structure Characterization of Escherichia coli Pseudouridine Kinase PsuK.
Front Microbiol, 13:926099-926099, 2022

PubMed Abstract: Pseudouridine (Ψ) is one of the most abundant RNA modifications in cellular RNAs that post-transcriptionally impact many aspects of RNA. However, the metabolic fate of modified RNA nucleotides has long been a question. A pseudouridine kinase (PsuK) and a pseudouridine monophosphate glycosylase (PsuG) in were first characterized as involved in pseudouridine degradation by catalyzing the phosphorylation of pseudouridine to pseudouridine 5'-phosphate (ΨMP) and further hydrolyzing 5'-ΨMP to produce uracil and ribose 5'-phosphate. Recently, their homolog proteins in eukaryotes were also identified, which were named PUKI and PUMY in . Here, we solved the crystal structures of apo-PsuK and its binary complex with Ψ or -methyl-pseudouridine (m1Ψ). The structure of PsuK showed a homodimer conformation assembled by its β-thumb region. PsuK has an appropriate binding site with a series of hydrophilic and hydrophobic interactions for Ψ. Moreover, our complex structure of PsuK-m1Ψ suggested the binding pocket has an appropriate capacity for m1Ψ. We also identified the monovalent ion-binding site and potential ATP-binding site. Our studies improved the understanding of the mechanism of Ψ turnover.

PubMed: 35783380
DOI: 10.3389/fmicb.2022.926099

実験手法

X-RAY DIFFRACTION (2.31 Å)