Strained Conformations of Nucleosides in Active Sites of Nucleoside Phosphorylases

Abstract

Nucleoside phosphorylases catalyze the reversible phosphorolysis of nucleosides to heterocyclic bases, giving α-d-ribose-1-phosphate or α-d-2-deoxyribose-1-phosphate. These enzymes are involved in salvage pathways of nucleoside biosynthesis. The level of these enzymes is often elevated in tumors, which can be used as a marker for cancer diagnosis. This review presents the analysis of conformations of nucleosides and their analogues in complexes with nucleoside phosphorylases of the first (NP-1) family, which includes hexameric and trimeric purine nucleoside phosphorylases (EC 2.4.2.1), hexameric and trimeric 5′-deoxy-5′-methylthioadenosine phosphorylases (EC 2.4.2.28), and uridine phosphorylases (EC 2.4.2.3). Nucleosides adopt similar conformations in complexes, with these conformations being significantly different from those of free nucleosides. In complexes, pentofuranose rings of all nucleosides are at the W region of the pseudorotation cycle that corresponds to the energy barrier to the N↔S interconversion. In most of the complexes, the orientation of the bases with respect to the ribose is in the high-syn region in the immediate vicinity of the barrier to syn ↔ anti transitions. Such conformations of nucleosides in complexes are unfavorable when compared to free nucleosides and they are stabilized by interactions with the enzyme. The sulfate (or phosphate) ion in the active site of the complexes influences the conformation of the furanose ring. The binding of nucleosides in strained conformations is a characteristic feature of the enzyme–substrate complex formation for this enzyme group.

Structure, Oligomerization and Activity Modulation in N-Ribohydrolases

“…A common strategy in most organisms is the cleavage of the N-glycosidic bond in nucleoside substrates via a phosphorolytic reaction catalyzed by a family of nucleoside phosphorylases (NPs) [ 15 , 16 ]. All NP enzymes bind an inorganic phosphate ion to the active site, directing its nucleophilic attack to the C1’ atom of the nucleoside substrate and yielding the free base and the ribosyl moiety linked to the negatively charged phosphate [ 17 ] that is thus retained in the cell cytosol.…”

Crystal structures of a new class of pyrimidine/purine nucleoside phosphorylase revealed a Cupin fold

“…1 The proposed enzymatic reaction for the purine/pyrimidine nucleosides was established previously, whereby the C N glycosidic bond is cleaved by a phosphate ion. 5 discovered 241 potential novel enzymes in Escherichia coli, 12 of which were experimentally validated. 6 One of these validated enzymes is Pyrimidine/purine nucleoside phosphorylase (ppnP), which is further identified to catalyze the phosphorolysis of diverse nucleosides such as uridine, adenosine, guanosine, cytidine, thymidine, inosine, and xanthosine as substrates, and yielding D-ribose 1-phosphate and the respective free bases.…”

“…Two families of nucleoside phosphorylases that catalyze the phosphorolytic cleavage of the glycosidic bond in nucleosides have been discovered, the trimeric or hexameric nucleoside phosphorylase‐I (NP‐I) family enzymes share a common α‐/β‐subunit fold and accept a range of purine nucleosides, as well as uridine nucleotide; and the nucleoside phosphorylase‐II (NP‐II) family enzymes that display dimeric structures and accept both thymidine and uridine in lower organisms, but are specific for thymidine in higher species 1 . The proposed enzymatic reaction for the purine/pyrimidine nucleosides was established previously, whereby the CN glycosidic bond is cleaved by a phosphate ion 5 …”

Interactions of 2,6-substituted purines with purine nucleoside phosphorylase from Helicobacter pylori in solution and in the crystal, and the effects of these compounds on cell cultures of this bacterium

“…Relatively recently, it was discovered that H. pylori also belongs to this class of microorganisms incapable of de novo purine synthesis 17 . Nucleoside phosphorylases play a key role in the salvage pathway 18 and, as far as we know, no one has tried to use inhibitors of the PNP to fight H. pylori infection. Therefore, in this study, we decided to check the influence of inhibitors of PNP from H. pylori on the growth rates of this bacterium in cell culture, and obtain a high-resolution three-dimensional structure of the enzyme-inhibitor complexes to characterise details of the enzyme-ligand interactions.…”