7EYM

Crystal structure of Vibrio cholerae ppnP

Summary for 7EYM

• Entry DOI: 10.2210/pdb7eym/pdb
• Descriptor: Pyrimidine/purine nucleoside phosphorylase (2 entities in total)
• Functional Keywords: pyrimidine, purine, nucleoside phosphorylase, hydrolase
• Biological source: Vibrio cholerae
• Total number of polymer chains: 2
• Total formula weight: 20546.89

Authors

Wen, Y.,Wu, B.X. (deposition date: 2021-05-31, release date: 2022-02-09, Last modification date: 2023-11-29)

Primary citation

Wen, Y.,Li, X.,Guo, W.,Wu, B.
Crystal structures of a new class of pyrimidine/purine nucleoside phosphorylase revealed a Cupin fold.
Proteins, 90:1233-1241, 2022

PubMed Abstract: Nucleotides metabolism is a fundamental process in all organisms. Two families of nucleoside phosphorylases (NP) that catalyze the phosphorolytic cleavage of the glycosidic bond in nucleosides have been found, including the trimeric or hexameric NP-I and dimeric NP-II family enzymes. Recent studies revealed another class of NP protein in Escherichia coli named Pyrimidine/purine nucleoside phosphorylase (ppnP), which can catalyze the phosphorolysis of diverse nucleosides and yield d-ribose 1-phosphate and the respective free bases. Here, we solved the crystal structures of ppnP from E. coli and the other three species. Our studies revealed that the structure of ppnP belongs to the RlmC-like Cupin fold and showed as a rigid dimeric conformation. Detail analysis revealed a potential nucleoside binding pocket full of hydrophobic residues, and the residues involved in the dimer and pocket formation are all well conserved in bacteria. Since the Cupin fold is a large superfamily in the biosynthesis of natural products, our studies provide the structural basis for understanding, and the directed evolution of NP proteins.

PubMed: 35094440
DOI: 10.1002/prot.26309

Experimental method

X-RAY DIFFRACTION (1.38 Å)