Pyrimidine nucleoside analogues as inducers of pyrimidine nucleoside catabolizing enzymes in Salmonella typhimurium

Protein-ligand interaction: grafting of the uridine-specific determinants from the CytR regulator of Salmonella typhimurium to Escherichia coli CytR

Members of the LacI family of transcriptional repressors respond to the presence of small effector molecules. The binding of the ligands affect the proteins ability to repress transcription by stabilizing a conformation that, in most cases, is unfavorable for high-affinity DNA binding. The CytR anti-activator diverges from the other family members by relying on the cooperative DNA binding with the global regulator CRP. The inducers of CytR do not affect CytR-DNA binding per se, but alleviate repression by interrupting protein-protein interactions between the two regulators. Here, we have studied of the CytR-inducer interaction by exploring a discrepancy in the inducer response observed for the homologous CytR regulators of Escherichia coli and Salmonella typhimurium. CytR of S. typhimurium (CytRSt) appears to respond to the presence of both uridine and cytidine nucleosides, whereas E. coli CytR (CytREc) responds to cytidine only. We have used a combination of genetic and structural modeling studies to provide detailed information regarding the nature of this discrepancy. By analysis of hybrid CytR proteins followed by site-directed mutagenesis, we have successfully transferred the specificity determinants for uridine from CytRSt to CytREc, revealing that serine substitutions of only two residues (G131 and A152) in CytREc is required to make CytREc sensitive to uridine. In addition, by employing a genetic screen for induction of defective mutants, we have identified four amino acid residues in CytRSt that appear to be important for the response to uridine. The implications of these findings for the understanding of the ligand binding and induction of CytR are discussed in the context of the structural knowledge of CytR and homologous protein-ligand complexes.

Pyrimidine ribonucleoside phosphorylase activity vs 5- and/or 6-substituted uracil and uridine analogues, including conformational aspects

The pyrimidine ribonucleoside phosphorylase from Salmonella typhimurium phosphorylyses 6-methyluridine, a uridine analogue sterically constrained to the syn conformation about the glycosylic bond, as effectively as uridine itself. In conjunction with the observation that 3-methyluridine is a very poor substrate compared to 5-methyluridine and 5,6-dimethyluridine, it follows that the phosphorolysis reaction involves the initial conversion of uridine, and other 5-substituted uridines (including 5-fluorouridine), to the syn conformation during interaction with the enzyme. Furthermore, and consistent with the foregoing, the enzyme recognizes as substrates, to varying degrees, the N(3)-ribosides of xanthine and uric acid, and will also catalyze the formation of these ribosides from the corresponding purines, which may be considered formally as 5,6-disubstituted uracils. Similar observations are reported for the synthetic 5,6-trimethyleneuridine. The enzyme does not, however, recognize 6-methyluracil and 5,6-tetramethyleneuridine in the reverse, synthetic, reaction. The conformational aspects of these reactions are discussed. Since it was previously shown that 6-methyluridine is an equally effective substrate for the pyrimidine phosphorylase of primary rabbit kidney cells, at least some of these conformational requirements apply to the enzyme from mammalian sources, and are consequently of relevance in the design of chemotherapeutic agents, for which some examples are cited.

Correlations of conformational parameters and equilibrium conformational states in a variety of beta-D-arabinonucleosides and their analogues

H nuclear magnetic resonance spectroscopy has been applied to a study of the conformations of a variety of purine and pyrimidine beta-D-arabinofuranosyl nucleosides. The experimental results, together with data collected from the literature, demonstrated the existence of reasonably good correlations between the coupling constants made it possible to define more accurately, than hitherto possible, the conformational states between which equilibria exist in solution. The equilibrium for the arabinonucleosides differs from that previously established for ribonucleosides; in particular, structural modifications and solvent effects may appreciably modify the conformational states between which equilibria exist. Preliminary measurements on some arabinosides in the syn conformation about the glycosidic bond indicated that these do not conform to the foregoing correlations, and will require separate study. A correlation has also been established between the conformation of the arabinose ring and that of the exocyclic 5'-CH2OH group. For both purine and pyrimidine arabinonucleosides, the conformational state 3E of the arabinose ring coexists to some extent with a gauche-gauche conformation of the exocyclic 5'-CH2OH, as in the case of pyrimidine (but not purine) ribonucleosides. Application of the foregoing to some biological problems is described.