7VSK
Crystal structure of E.coli pseudouridine kinase PsuK complexed with pseudouridine.
Summary for 7VSK
| Entry DOI | 10.2210/pdb7vsk/pdb |
| Descriptor | 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) |
| Functional Keywords | pseudouridine, kinase, yeic, rna binding protein |
| Biological source | Escherichia coli (strain B / BL21-DE3) |
| Total number of polymer chains | 1 |
| Total formula weight | 34025.29 |
| Authors | |
| 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 Cited by 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: 35783380DOI: 10.3389/fmicb.2022.926099 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.31 Å) |
Structure validation
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