6F4X

Crystal structure of H. pylori purine nucleoside phosphorylase in complex with PO4 and formycin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 

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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: https://doi.org/10.1111/febs.14403
  • Primary Citation of Related Structures:  
    5LU0, 6F4W, 6F4X, 6F52, 6F5A, 6F5I

  • 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 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. The atomic coordinates and structure factors have been deposited in the Protein Data Bank: with accession codes 6F52 (HpPNPapo_1), 6F5A (HpPNPapo_2), 6F5I (HpPNPapo_3), 5LU0 (HpPNP_PO4), 6F4W (HpPNP_FA) and 6F4X (HpPNP_PO4_FA). Purine nucleoside orthophosphate ribosyl transferase, EC2.4.2.1, UniProtID: P56463.


  • Organizational Affiliation

    Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Poland.


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 pyloriMutation(s): 0 
Gene Names: deoDHP_1178
EC: 2.4.2.1
UniProt
Find proteins for P56463 (Helicobacter pylori (strain ATCC 700392 / 26695))
Explore P56463 
Go to UniProtKB:  P56463
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56463
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMC
Query on FMC

Download Ideal Coordinates CCD File 
G [auth A]
N [auth B]
Q [auth C]
S [auth D]
X [auth E]
G [auth A],
N [auth B],
Q [auth C],
S [auth D],
X [auth E],
Z [auth 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
PO4
Query on PO4

Download Ideal Coordinates CCD File 
H [auth A],
P [auth C],
W [auth E]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth F]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
AA [auth F],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
O [auth B],
R [auth C],
T [auth D],
U [auth D],
V [auth D],
Y [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.893α = 90
b = 85.895β = 90
c = 269.306γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • 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
Poland--

Revision History  (Full details and data files)

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