3ONV: Crystal structure of E. Coli purine nucleoside phosphorylase with SO4

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.
PDB ID: 3ONVDownload
MMDB ID: 91545
PDB Deposition Date: 2010/8/30
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 1.893  Å
Source Organism:
Similar Structures:
Biological Unit for 3ONV: hexameric; determined by author and by software (PISA)
Molecular Components in 3ONV
Label Count Molecule
Proteins (6 molecules)
Purine Nucleoside Phosphorylase Deod-type
Molecule annotation
Chemicals (10 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB