7W93

Crystal structure of E.coli pseudouridine kinase PsuK complexed with N1-methyl-pseudouridine

Summary for 7W93

• Entry DOI: 10.2210/pdb7w93/pdb
• Descriptor: PfkB domain protein, 5-[(2S,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1-methyl-pyrimidine-2,4-dione, POTASSIUM ION, ... (4 entities in total)
• Functional Keywords: kinase, sugar, pseudouridine, m1-pseudouridine, mrna vaccine, sugar binding protein
• Biological source: Escherichia coli BL21(DE3)
• Total number of polymer chains: 1
• Total formula weight: 34078.42

Authors

Li, K.J.,Li, X.J.,Wu, B.X. (deposition date: 2021-12-09, release date: 2022-06-22, Last modification date: 2023-11-29)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.9 Å)