PDBsum entry 4ts3

Transferase

PDB id: 4ts3

Contents

Protein chains

(+ 0 more) 237 a.a.

Ligands

FMC ×2

PO4 ×6

Waters ×805

PDB id:

4ts3

Name:

Transferase

Title:

Wild type e. Coli purine nucleoside phosphorylase with 2 fmc molecules in active sites

Structure:

Purine nucleoside phosphorylase deod-type. Chain: a, b, c, d, e, f. Synonym: pnp. Ec: 2.4.2.1

Source:

Escherichia coli. Organism_taxid: 562

Resolution:

2.30Å R-factor: 0.180 R-free: 0.239

Authors:

Z.Stefanic,A.Bzowska

Key ref:

Z.Štefanić et al. (2018). Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis. Sci Rep, 8, 15427. PubMed id: 30337572

Date:

18-Jun-14 Release date: 08-Jul-15

Protein chains

P0ABP8  (DEOD_ECOLI) -  Purine nucleoside phosphorylase DeoD-type from Escherichia coli (strain K12)

Seq: 239 a.a.

Struc: 237 a.a.

Enzyme reactions

• Enzyme class: E.C.2.4.2.1 - purine-nucleoside phosphorylase.
• Reaction:
  1. a purine D-ribonucleoside + phosphate = a purine nucleobase + alpha- D-ribose 1-phosphate
  2. a purine 2'-deoxy-D-ribonucleoside + phosphate = a purine nucleobase + 2-deoxy-alpha-D-ribose 1-phosphate

purine D-ribonucleoside + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly) = purine nucleobase + alpha- D-ribose 1-phosphate

purine 2'-deoxy-D-ribonucleoside + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly) = purine nucleobase + 2-deoxy-alpha-D-ribose 1-phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Sci Rep 8:15427 (2018)

PubMed id: 30337572

Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis.

Z.Štefanić, M.Narczyk, G.Mikleušević, S.Kazazić, A.Bzowska, M.Luić.

ABSTRACT

Purine nucleoside phosphorylase (PNP) catalyses the cleavage of the glycosidic bond of purine nucleosides using phosphate instead of water as a second substrate. PNP from Escherichia coli is a homohexamer, build as a trimer of dimers, and each subunit can be in two conformations, open or closed. This conformational change is induced by the presence of phosphate substrate, and very likely a required step for the catalysis. Closing one active site strongly affects the others, by a yet unclear mechanism and order of events. Kinetic and ligand binding studies show strong negative cooperativity between subunits. Here, for the first time, we managed to monitor the sequence of nucleoside binding to individual subunits in the crystal structures of the wild-type enzyme, showing that first the closed sites, not the open ones, are occupied by the nucleoside. However, two mutations within the active site, Asp204Ala/Arg217Ala, are enough not only to significantly reduce the effectiveness of the enzyme, but also reverse the sequence of the nucleoside binding. In the mutant the open sites, neighbours in a dimer of those in the closed conformation, are occupied as first. This demonstrates how important for the effective catalysis of Escherichia coli PNP is proper subunit cooperation.