Xanthosine 5′-monophosphate (XMP). Acid–base and metal ion-binding properties of a chameleon-like nucleotide

Abstract

The four acidity constants of threefold protonated xanthosine 5′-monophosphate, H₃(XMP)⁺, reveal that in the physiological pH range around 7.5 (X − H·MP)³⁻ strongly dominates and not XMP²⁻ as commonly given in textbooks and often applied in research papers. Therefore, this nucleotide, which participates in many metabolic processes, should be addressed as xanthosinate 5′-monophosphate as is stated in this critical review. Micro acidity constant schemes allow quantification of intrinsic site basicities. In 9-methylxanthine nucleobase deprotonation occurs to more than 99% at (N3)H, whereas for xanthosine it is estimated that about 30% are (N1)H deprotonated and for (X − H·MP)³⁻ it is suggested that (N1)H deprotonation is further favored, especially in macrochelates where the phosphate-coordinated M²⁺ interacts with N7. The formation degree of these macrochelates in the (X − H·MP·M)⁻ species of Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺ or Cd²⁺ amounts to 90% or more. In the monoprotonated (M·X − H·MP·H)^± complexes, M²⁺ is located at the N7/[(C6)O] unit as the primary binding site and it forms macrochelates with the P(O)₂(OH)⁻ group to about 65% for nearly all metal ions considered (i.e., including Ba²⁺, Sr²⁺, Ca²⁺, Mg²⁺); this indicates outer-sphere binding to P(O)₂(OH)⁻. Finally, a new method quantifying the chelate effect is applied to the M(X − H·MP)⁻ species, stabilities and structures of mixed-ligand complexes are considered, and the stability constants for several M(X − H·DP)²⁻ and M(X − H·TP)³⁻ complexes are estimated (112 references).