6F4W

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

Summary for 6F4W

• Entry DOI: 10.2210/pdb6f4w/pdb
• Related: 5LU0
• Descriptor: Purine nucleoside phosphorylase DeoD-type, (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol (3 entities in total)
• Functional Keywords: purine nucleoside phosphorylase, h. pylori, formycin a, hydrolase
• Biological source: Helicobacter pylori (Campylobacter pylori)
• Total number of polymer chains: 6
• Total formula weight: 156512.08

Authors

Stefanic, Z. (deposition date: 2017-11-30, release date: 2018-02-14, Last modification date: 2024-01-17)

Primary citation

Narczyk, M.,Bertosa, B.,Papa, L.,Vukovic, V.,Lescic Asler, I.,Wielgus-Kutrowska, B.,Bzowska, A.,Luic, M.,Stefanic, Z.
Helicobacter pylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features.
FEBS J., 285:1305-1325, 2018

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 ) 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 binding, while a three-site model is needed to characterize FA binding, irrespective of P presence. The latter may be related to the newly found nonstandard mode of FA binding. The ternary complex of the enzyme with P and FA shows, however, that P binding stabilizes the standard mode of FA binding. Surprisingly, HpPNP has low affinity towards the natural substrate adenosine. Molecular dynamics simulations show that P 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.

PubMed: 29430816
DOI: 10.1111/febs.14403

Experimental method

X-RAY DIFFRACTION (2.293 Å)