5MX8

Crystal structure of H. pylori purine nucleoside phosphorylase from clinical isolate HpPNP-3

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

  • Deposited: 2017-01-21 Released: 2017-04-05 
  • Deposition Author(s): Stefanic, Z.
  • Funding Organization(s): Croatian Science Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

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: 10.1016/j.ijbiomac.2017.03.101
  • Structures With Same Primary Citation

  • 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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase DeoD-typeA233Helicobacter pyloriMutation(s): 0 
EC: 2.4.2.1
Find proteins for P56463 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56463 
Go to UniProtKB:  P56463
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
HPA
Query on HPA

Download CCD File 
A
HYPOXANTHINE
C5 H4 N4 O
FDGQSTZJBFJUBT-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.596α = 90
b = 143.596β = 90
c = 143.596γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
CrysalisProdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-01-21 
  • Released Date: 2017-04-05 
  • Deposition Author(s): Stefanic, Z.

Funding OrganizationLocationGrant Number
Croatian Science FoundationCroatia7423

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection