5MX4

Crystal structure of H. pylori purine nucleoside phosphorylase from clinical isolate HpPNP-1

  • Classification: TRANSFERASE
  • Organism(s): Helicobacter pylori R018c
  • Mutation(s): No 

  • Deposited: 2017-01-20 Released: 2017-04-05 
  • Deposition Author(s): Stefanic, Z.
  • Funding Organization(s): Croatian Science Foundation, FP7/2007-2013, Biostruct-X

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural characterization of purine nucleoside phosphorylase from human pathogen Helicobacter pylori.

Stefanic, Z.Mikleusevic, G.Luic, M.Bzowska, A.Lescic Asler, I.

(2017) Int J Biol Macromol 101: 518-526

  • DOI: https://doi.org/10.1016/j.ijbiomac.2017.03.101
  • Primary Citation of Related Structures:  
    5MX4, 5MX6, 5MX8

  • PubMed Abstract: 

    Microaerophilic bacterium Helicobacer pylori is a well known human pathogen involved in the development of many diseases. Due to the evergrowing infection rate and increase of H. pylori antibiotic resistence, it is of utmost importance to find a new way to attack and eradicate H. pylori. The purine metabolism in H. pylori is solely dependant on the salvage pathway and one of the key enzymes in this pathway is purine nucleoside phosphorylase (PNP). In this timely context, we report here the basic biochemical and structural characterization of recombinant PNP from the H. pylori clinical isolate expressed in Escherichia coli. Structure of H. pylori PNP is typical for high molecular mass PNPs. However, its activity towards adenosine is very low, thus resembling more that of low molecular mass PNPs. Understanding the molecular mechanism of this key enzyme may lead to the development of new drug strategies and help in the eradication of H. pylori.


  • Organizational Affiliation

    Division of Physical Chemistry, Ruđer Bošković Institute, POB 180, Bijenička cesta 54, HR-10002 Zagreb, Croatia.


Macromolecules
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 pylori R018cMutation(s): 0 
EC: 2.4.2.1 (PDB Primary Data), 2.4.2.3 (UniProt)
UniProt
Find proteins for K2JXG0 (Helicobacter pylori R018c)
Explore K2JXG0 
Go to UniProtKB:  K2JXG0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK2JXG0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.19α = 90
b = 129.492β = 90
c = 156.019γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2017-04-05 
  • Deposition Author(s): Stefanic, Z.

Funding OrganizationLocationGrant Number
Croatian Science FoundationCroatia7423
FP7/2007-2013, Biostruct-X283570

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description