Crystal structure of Vibrio cholerae ppnP

Experimental Data Snapshot

  • Resolution: 1.38 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

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This is version 1.3 of the entry. See complete history


Crystal structures of a new class of pyrimidine/purine nucleoside phosphorylase revealed a Cupin fold.

Wen, Y.Li, X.Guo, W.Wu, B.

(2022) Proteins 90: 1233-1241

  • DOI: https://doi.org/10.1002/prot.26309
  • Primary Citation of Related Structures:  
    7EYJ, 7EYK, 7EYL, 7EYM, 7EYP

  • 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.

  • Organizational Affiliation

    Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, RNA Biomedical Institute, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrimidine/purine nucleoside phosphorylase
A, B
96Vibrio choleraeMutation(s): 0 
Gene Names: ppnP
Find proteins for Q9KKY0 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KKY0 
Go to UniProtKB:  Q9KKY0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KKY0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.38 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.242α = 90
b = 55.242β = 90
c = 111.851γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2022-05-04
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description