6F4W

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.293 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1111/febs.14403
  • Primary Citation of Related Structures:  

  • 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 ...

    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 Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia.,Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Poland.,Department of Chemistry, Faculty of Science, University of 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 (strain ATCC 700392 / 26695)Mutation(s): 0 
Gene Names: deoD
EC: 2.4.2.1
Find proteins for P56463 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  P56463
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMC
Query on FMC

Download SDF File 
Download CCD File 
A, B, C, D, E, F
(1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol
C10 H13 N5 O4
KBHMEHLJSZMEMI-KSYZLYKTSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.293 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.051α = 90.00
b = 84.801β = 90.00
c = 274.462γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-11-30 
  • 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 

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-02-21
    Type: Database references
  • Version 1.2: 2018-04-25
    Type: Data collection, Database references