5LU0

Crystal structure of H. pylori referent strain in complex with PO4

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

  • Deposited: 2016-09-07 Released: 2017-09-20 
  • Deposition Author(s): Stefanic, Z.
  • Funding Organization(s): Croatian science foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase DeoD-typeA, B, C, D, E, F233Helicobacter 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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download CCD File 
A, B, C, E
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B, C, E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B, C, D, E, F
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.52α = 90
b = 86.31β = 90
c = 268.449γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
iMOSFLMdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-09-07 
  • Released Date: 2017-09-20 
  • Deposition Author(s): Stefanic, Z.

Funding OrganizationLocationGrant Number
Croatian science foundationCroatia7423

Revision History 

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Database references
  • Version 1.2: 2018-02-21
    Changes: Database references
  • Version 1.3: 2018-04-25
    Changes: Data collection, Database references