3ONV

Crystal structure of E. Coli purine nucleoside phosphorylase with SO4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.893 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Validation of the catalytic mechanism of Escherichia coli purine nucleoside phosphorylase by structural and kinetic studies.

Mikleusevic, G.Stefanic, Z.Narczyk, M.Wielgus-Kutrowska, B.Bzowska, A.Luic, M.

(2011) Biochimie 93: 1610-1622

  • DOI: 10.1016/j.biochi.2011.05.030
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The catalytic mechanism of Escherichia coli purine nucleoside phosphorylase (PNP) is revised using site-directed mutagenesis, kinetic studies and structure determinations. The experimental evidence on the role of the particular catalytic amino acid d ...

    The catalytic mechanism of Escherichia coli purine nucleoside phosphorylase (PNP) is revised using site-directed mutagenesis, kinetic studies and structure determinations. The experimental evidence on the role of the particular catalytic amino acid during catalysis has not been available. Therefore, the active site mutants Arg24Ala, Asp204Ala, Asp204Asn, Arg217Ala and Asp204Ala/Arg217Ala were prepared and their kinetics and thermodynamic studies were carried out. The activity tests with natural substrates and 7-methylguanosine confirmed the earlier hypothesis, that catalysis involves protonation of the purine base at position N7 by Asp204, which is triggered by Arg217. The crystal structures of the wild type in complexes with phosphate and sulphate, respectively, and of the Arg24Ala mutant in complex with phosphate/sulphate were determined. The structural data show that previously observed conformational change is a result of the phosphate binding and its interaction with Arg24. As E. coli PNP is a promising candidate for the tumour-directed gene therapy, our results may also help to design efficient mutants useful in gene therapy.


    Organizational Affiliation

    Division of Physical Chemistry, Ruđer Bošković Institute, POB 180, HR-10002 Zagreb, Croatia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Purine nucleoside phosphorylase deoD-type
A, B, C
237Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: deoD (pup)
EC: 2.4.2.1
Find proteins for P0ABP8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABP8
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.893 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.175 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 120.304α = 90.00
b = 120.304β = 90.00
c = 239.809γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXphasing
XDSdata reduction
MAR345data collection
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-13
    Type: Initial release
  • Version 1.1: 2013-08-14
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description