8K05

Pseudouridine 5'-monophosphate glycosylase from Arabidopsis thaliana -- sulfate bound holoenzyme

Summary for 8K05

• Entry DOI: 10.2210/pdb8k05/pdb
• Descriptor: Pseudouridine-5'-phosphate glycosidase, MANGANESE (II) ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: metalloenzyme, glycosylase, c-nucleoside, pseudouridine monophosphate, metal binding protein, hydrolase
• Biological source: Arabidopsis thaliana (thale cress)
• Total number of polymer chains: 1
• Total formula weight: 36429.15

Authors

Lee, J.Y.,Kim, S.H.,Rhee, S.K. (deposition date: 2023-07-07, release date: 2024-05-15)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.45 Å)