scholarly journals Crystal structures of a new class of pyrimidine/purine nucleoside phosphorylase (ppnP) revealed a Cupin fold

2021 ◽  
Author(s):  
Yan Wen ◽  
Xiaojia Li ◽  
Wenting Guo ◽  
Baixing Wu
Keyword(s):  
Crystal Structures ◽  
Purine Nucleoside Phosphorylase ◽  
Binding Pocket ◽  
Purine Nucleoside ◽  
Structural Basis ◽  
Nucleoside Phosphorylase ◽  
E Coli ◽  
New Class ◽  
Nucleoside Phosphorylases ◽  
Pocket Formation

Nucleotides metabolism is a fundamental process in all organisms. Two families of nucleoside phosphorylases (NP) that catalyze the phosphorolytic cleavage of the glycosidic bond in nucleosides have been found, including the trimeric or hexameric NP-I and dimeric NP-II family enzymes. Recently studies revealed another class of NP protein in E. coli named Pyrimidine/purine nucleoside phosphorylase (ppnP), which can catalyze the phosphorolysis of diverse nucleosides and yield D-ribose 1-phosphate and the respective free bases. Here, we solve the crystal structures of ppnP from E. coli and the other three species. Our studies revealed that the structure of ppnP belongs to the Rlmc-like cupin fold and showed as a rigid dimeric conformation. Detail analysis revealed a potential nucleoside binding pocket full of hydrophobic residues. And the residues involved in the dimer and pocket formation are all well conserved in bacteria. Since the cupin fold is a large superfamily in the biosynthesis of natural products, our studies provide the structural basis for understanding and the directed evolution of NP proteins.

scholarly journals Radical Dehalogenation and Purine Nucleoside Phosphorylase E. coli: How Does an Admixture of 2′,3′-Anhydroinosine Hinder 2-fluoro-cordycepin Synthesis

Biomolecules ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 539
Author(s):  
Alexey L. Kayushin ◽  
Julia A. Tokunova ◽  
Ilja V. Fateev ◽  
Alexandra O. Arnautova ◽  
Maria Ya. Berzina ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Chemical Synthesis ◽  
Purine Nucleoside Phosphorylase ◽  
Purine Nucleoside ◽  
Preparative Synthesis ◽  
Nucleoside Phosphorylase ◽  
E Coli ◽  
First Time

During the preparative synthesis of 2-fluorocordycepin from 2-fluoroadenosine and 3′-deoxyinosine catalyzed by E. coli purine nucleoside phosphorylase, a slowdown of the reaction and decrease of yield down to 5% were encountered. An unknown nucleoside was found in the reaction mixture and its structure was established. This nucleoside is formed from the admixture of 2′,3′-anhydroinosine, a byproduct in the preparation of 3-′deoxyinosine. Moreover, 2′,3′-anhydroinosine forms during radical dehalogenation of 9-(2′,5′-di-O-acetyl-3′-bromo- -3′-deoxyxylofuranosyl)hypoxanthine, a precursor of 3′-deoxyinosine in chemical synthesis. The products of 2′,3′-anhydroinosine hydrolysis inhibit the formation of 1-phospho-3-deoxyribose during the synthesis of 2-fluorocordycepin. The progress of 2′,3′-anhydroinosine hydrolysis was investigated. The reactions were performed in D2O instead of H2O; this allowed accumulating intermediate substances in sufficient quantities. Two intermediates were isolated and their structures were confirmed by mass and NMR spectroscopy. A mechanism of 2′,3′-anhydroinosine hydrolysis in D2O is fully determined for the first time.

Localization of purine and pyrimidine nucleoside phosphorylases in heart, kidney, and liver

1980 ◽  
Vol 239 (6) ◽  
pp. H721-H730 ◽  
Author(s):  
R. Rubio ◽  
R. M. Berne
Keyword(s):  
Guinea Pig ◽  
Kupffer Cells ◽  
Cellular Localization ◽  
Purine Nucleoside Phosphorylase ◽  
Degradation Products ◽  
Purine Nucleoside ◽  
Capillary Endothelium ◽  
Cell Fractionation ◽  
Nucleoside Phosphorylase ◽  
Nucleoside Phosphorylases

In isolated livers and kidneys perfused with Krebs-Henseleit solution, the relationship of the concentration of adenosine (Ado) to that of its degradation products inosine (Ino) and hypoxanthine (Hyp) in biliary, urinary, and venous effluents were determined. They revealed ratios of Hyp:Ado:Ino, 1.9:1:0.9, 0.7:1:0.6, and 1.3:1:0.5 for guinea pig biliary, guinea pig urinary, and rat urinary effluents, respectively, and their respective venous effluent were 58:1:29, 8.6:1:5.4, and 7.4:1:3.2. The greater proportion of Ino and Hyp in the venous effluents suggests active production in Ino and Hyp at the vessel wall. Purine nucleoside phosphorylase localization was determined histochemically and found most active in the cytoplasm of capillary endothelium and Kupffer cells. Thus, there is agreement between purine analysis and histochemical findings. The reliability of the histochemical technique was also tested by comparing activities of purine nucleoside phosphorylase (a cytoplasmic enzyme) and pyrmidine nucleoside phosphorylase (a nuclear enzyme) that catalyze similar reactions (nucleoside + inorganic phosphate in equilibrium base + ribose-1-phosphate) but with different base specificites and cellular localization, as indicated by cell fractionation studies. The histochemical results show that in contrast to the purine nucleoside phosphorylase, the pyrmidine specific enzyme was most active in the nuclei of endothelial and Kupffer cells. Thus, the technique discriminates between the two enzymes.

Adenosine binding to low-molecular-weight purine nucleoside phosphorylase: the structural basis for recognition based on its complex with the enzyme fromSchistosoma mansoni

2009 ◽  
Vol 66 (1) ◽  
pp. 73-79 ◽  
Author(s):  
Humberto M. Pereira ◽  
Martha M. Rezende ◽  
Marcelo Santos Castilho ◽  
Glaucius Oliva ◽  
Richard C. Garratt
Keyword(s):  
Molecular Weight ◽  
Purine Nucleoside Phosphorylase ◽  
De Novo ◽  
Purine Nucleoside ◽  
Structural Basis ◽  
Low Molecular Weight ◽  
Salvage Pathway ◽  
Structural Explanation ◽  
Nucleoside Phosphorylase ◽  
Transition State Analogues

Schistosomes are unable to synthesize purinesde novoand depend exclusively on the salvage pathway for their purine requirements. It has been suggested that blockage of this pathway could lead to parasite death. The enzyme purine nucleoside phosphorylase (PNP) is one of its key components and molecules designed to inhibit the low-molecular-weight (LMW) PNPs, which include both the human and schistosome enzymes, are typically analogues of the natural substrates inosine and guanosine. Here, it is shown that adenosine both binds toSchistosoma mansoniPNP and behaves as a weak micromolar inhibitor of inosine phosphorolysis. Furthermore, the first crystal structures of complexes of an LMW PNP with adenosine and adenine are reported, together with those with inosine and hypoxanthine. These are used to propose a structural explanation for the selective binding of adenosine to some LMW PNPs but not to others. The results indicate that transition-state analogues based on adenosine or other 6-amino nucleosides should not be discounted as potential starting points for alternative inhibitors.

scholarly journals In vivo sensitization of ovarian tumors to chemotherapy by expression of E. coli purine nucleoside phosphorylase in a small fraction of cells

Gene Therapy ◽  
2000 ◽  
Vol 7 (20) ◽  
pp. 1738-1743 ◽  
Author(s):  
V K Gadi ◽  
S D Alexander ◽  
J E Kudlow ◽  
P Allan ◽  
W B Parker ◽  
...  
Keyword(s):  
Purine Nucleoside Phosphorylase ◽  
Ovarian Tumors ◽  
Purine Nucleoside ◽  
Nucleoside Phosphorylase ◽  
E Coli
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