Crystal structure of H. pylori purine nucleoside phosphorylase in complex with formycin A

  • Classification: HYDROLASE
  • Organism(s): Helicobacter pylori
  • Expression System: Escherichia coli BL21
  • Mutation(s): No 

  • Deposited: 2017-11-30 Released: 2018-02-14 
  • Deposition Author(s): Stefanic, Z.
  • Funding Organization(s): Croatian Science Founataion, National Science Center of Poland, Polish Ministry for Science and Higher Education

Experimental Data Snapshot

  • Resolution: 2.29 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

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Helicobacter pylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features.

Narczyk, M.Bertosa, B.Papa, L.Vukovic, V.Lescic Asler, I.Wielgus-Kutrowska, B.Bzowska, A.Luic, M.Stefanic, Z.

(2018) FEBS J 285: 1305-1325

  • DOI: https://doi.org/10.1111/febs.14403
  • Primary Citation of Related Structures:  
    5LU0, 6F4W, 6F4X, 6F52, 6F5A, 6F5I

  • PubMed Abstract: 

    Even with decades of research, purine nucleoside phosphorylases (PNPs) are enzymes whose mechanism is yet to be fully understood. This is especially true in the case of hexameric PNPs, and is probably, in part, due to their complex oligomeric nature and a whole spectrum of active site conformations related to interactions with different ligands. Here we report an extensive structural characterization of the apo forms of hexameric PNP from Helicobacter pylori (HpPNP), as well as its complexes with phosphate (P i ) and an inhibitor, formycin A (FA), together with kinetic, binding, docking and molecular dynamics studies. X-ray structures show previously unseen distributions of open and closed active sites. Microscale thermophoresis results indicate that a two-site model describes P i binding, while a three-site model is needed to characterize FA binding, irrespective of P i presence. The latter may be related to the newly found nonstandard mode of FA binding. The ternary complex of the enzyme with P i and FA shows, however, that P i binding stabilizes the standard mode of FA binding. Surprisingly, HpPNP has low affinity towards the natural substrate adenosine. Molecular dynamics simulations show that P i moves out of most active sites, in accordance with its weak binding. Conformational changes between nonstandard and standard binding modes of nucleoside are observed during the simulations. Altogether, these findings show some unique features of HpPNP and provide new insights into the functioning of the active sites, with implications for understanding the complex mechanism of catalysis of this enzyme.

  • Organizational Affiliation

    Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Poland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Purine nucleoside phosphorylase DeoD-type
A, B, C, D, E
A, B, C, D, E, F
233Helicobacter pyloriMutation(s): 0 
Gene Names: deoDHP_1178
Find proteins for P56463 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56463 
Go to UniProtKB:  P56463
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56463
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.29 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.051α = 90
b = 84.801β = 90
c = 274.462γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2018-02-14 
  • Deposition Author(s): Stefanic, Z.

Funding OrganizationLocationGrant Number
Croatian Science FounataionCroatia7423
National Science Center of PolandPoland2015/18/M/NZ1/00776
Polish Ministry for Science and Higher EducationPolandBST-173300/BF

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description