5I3C

Crystal structure of E.coli purine nucleoside phosphorylase with acycloguanosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Crystal structure of Escherichia coli purine nucleoside phosphorylase complexed with acyclovir.

Timofeev, V.I.Zhukhlistova, N.E.Abramchik, Y.A.Muravieva, T.I.Esipov, R.S.Kuranova, I.P.

(2018) Acta Crystallogr F Struct Biol Commun 74: 402-409

  • DOI: 10.1107/S2053230X18008087

  • PubMed Abstract: 
  • Escherichia coli purine nucleoside phosphorylase (PNP), which catalyzes the reversible phosphorolysis of purine ribonucleosides, belongs to the family I hexameric PNPs. Owing to their key role in the purine salvage pathway, PNPs are attractive target ...

    Escherichia coli purine nucleoside phosphorylase (PNP), which catalyzes the reversible phosphorolysis of purine ribonucleosides, belongs to the family I hexameric PNPs. Owing to their key role in the purine salvage pathway, PNPs are attractive targets for drug design against some pathogens. Acyclovir (ACV) is an acyclic derivative of the PNP substrate guanosine and is used as an antiviral drug for the treatment of some human viral infections. The crystalline complex of E. coli PNP with acyclovir was prepared by co-crystallization in microgravity using counter-diffusion through a gel layer in a capillary. The structure of the E. coli PNP-ACV complex was solved at 2.32 Å resolution using the molecular-replacement method. The ACV molecule is observed in two conformations and sulfate ions were located in both the nucleoside-binding and phosphate-binding pockets of the enzyme. A comparison with the complexes of other hexameric and trimeric PNPs with ACV shows the similarity in acyclovir binding by these enzymes.


    Organizational Affiliation

    Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics' of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase DeoD-type
A, B, C
237Escherichia coli O139:H28 (strain E24377A / ETEC)Mutation(s): 0 
Gene Names: deoD
EC: 2.4.2.1
Find proteins for A7ZVS7 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Go to UniProtKB:  A7ZVS7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
AC2
Query on AC2

Download SDF File 
Download CCD File 
A, B, C
9-HYROXYETHOXYMETHYLGUANINE
C8 H11 N5 O3
MKUXAQIIEYXACX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.176 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 120.030α = 90.00
b = 120.030β = 90.00
c = 238.141γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-22
    Type: Initial release
  • Version 2.0: 2018-07-11
    Type: Atomic model, Data collection, Database references