5MX4

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.ijbiomac.2017.03.101
  • Primary Citation of Related Structures:  

  • 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 ...

    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. Electronic address: ivana.lescic.asler@irb.hr.,Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Żwirki i Wigury 93, 02-089 Warsaw, Poland.,Division of Physical Chemistry, Ruđer Bošković Institute, POB 180, Bijenička cesta 54, HR-10002 Zagreb, Croatia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase DeoD-type
A, B, C, D, E, F
233Helicobacter pylori R018cMutation(s): 0 
Gene Names: deoD
EC: 2.4.2.1
Find proteins for K2JXG0 (Helicobacter pylori R018c)
Go to UniProtKB:  K2JXG0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
HPA
Query on HPA

Download SDF File 
Download CCD File 
C
HYPOXANTHINE
C5 H4 N4 O
FDGQSTZJBFJUBT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.190α = 90.00
b = 129.492β = 90.00
c = 156.019γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-01-20 
  • Released Date: 2017-04-05 
  • Deposition Author(s): Stefanic, Z.

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

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-12
    Type: Database references