Comparison of two hydrated forms of sodium inosine 5'-monophosphate

The features of the crystal structure of the layered series hydrates of uridine-5'-monophosphate salts (UMPNa x ·yH2O)

Almost all reported salts of nucleotides crystallized from solutions are in the form of hydrate. Layered hydrates often occur in crystals with more than five water molecules per host molecule. In the present report, five single-crystal structures of uridine-5'-monophosphate (UMP) series hydrates of acid or salts (UMPNa _x ·yH₂O, x = 0-2) were determined and analysed. It was found that all crystal hydrates were orthorhombic with a C222₁ space group but with mere variation in the plane angle of adjacent bases and the distance between phosphate arms. The packing arrangements of UMPNa _x ·yH₂O hydrates present typical layered sandwich structures and show that the UMP molecular layers alternate with water molecular layers parallel to the ac plane, linked by hydrogen bonds or coupled with coordinate bonds besides ionic electrostatic interaction. Metal ions were located in water molecular layers as a form of hydration. In addition, we tried to deduce and give insights into the formation of UMPNa _x ·yH₂O hydrates. The effect of water molecules and metal ions on the crystal structure and stability was investigated. It was found that the coexistence of relatively rigid architectures constructed by host molecules and flexible interlayer regions was a key factor to the formation of these hydrates. Excessive loss of lattice water would give rise to the irreversible collapse of the host structure and loss of ability to recover to the initial state under humidity. Approximately seven crystal-water molecules were the balance point of sodium salt hydrates at room temperature under 43-76% RH conditions. The number of sodium ions in the crystal lattice is positively correlated with their thermal stability.

23Na double-rotation NMR of sodium nucleotides leads to the discovery of a new dCMP hendecahydrate

Obtaining definitive information concerning the coordination environment of sodium ions which balance the negative charges found in nucleotides is a challenging task. We show that high resolution 1D and 2D (23)Na NMR spectra of sodium nucleotides obtained in the solid state with the use of double-rotation (DOR) provide valuable structural information. Sensitive spin diffusion homonuclear correlation experiments are used to establish the relative proximities of various pairs of crystallographically distinct Na sites and to assign the spectral resonances. Additionally, the DOR sidebands are simulated to obtain coordination information which is complementary to that obtained using multiple-quantum magic-angle spinning NMR spectra. These experiments led us to discover a new hendecahydrate of deoxycytidine monophosphate (dCMP), the structure of which is confirmed via single-crystal X-ray diffraction. This hydrate crystallizes reproducibly when deuterated water is used exclusively in the preparation process.

Activator anion binding site in pyridoxal phosphorylase b: the binding of phosphite, phosphate, and fluorophosphate in the crystal

It has been established that phosphate analogues can activate glycogen phosphorylase reconstituted with pyridoxal in place of the natural cofactor pyridoxal 5'-phosphate (Change YC. McCalmont T, Graves DJ. 1983. Biochemistry 22:4987-4993). Pyridoxal phosphorylase b has been studied by kinetic, ultracentrifugation, and X-ray crystallographic experiments. In solution, the catalytically active species of pyridoxal phosphorylase b adopts a conformation that is more R-state-like than that of native phosphorylase b, but an inactive dimeric species of the enzyme can be stabilized by activator phosphite in combination with the T-state inhibitor glucose. Co-crystals of pyridoxal phosphorylase b complexed with either phosphite, phosphate, or fluorophosphate, the inhibitor glucose, and the weak activator IMP were grown in space group P4(3)2(1)2, with native-like unit cell dimensions, and the structures of the complexes have been refined to give crystallographic R factors of 18.5-19.2%, for data between 8 and 2.4 A resolution. The anions bind tightly at the catalytic site in a similar but not identical position to that occupied by the cofactor 5'-phosphate group in the native enzyme (phosphorus to phosphorus atoms distance = 1.2 A). The structural results show that the structures of the pyridoxal phosphorylase b-anion-glucose-IMP complexes are overall similar to the glucose complex of native T-state phosphorylase b. Structural comparisons suggest that the bound anions, in the position observed in the crystal, might have a structural role for effective catalysis.

N-acetyl-beta-D-glucopyranosylamine: a potent T-state inhibitor of glycogen phosphorylase. A comparison with alpha-D-glucose

Structure-based drug design has led to the discovery of a number of glucose analogue inhibitors of glycogen phosphorylase that have an increased affinity compared to alpha-D-glucose (Ki = 1.7 mM). The best inhibitor in the class of N-acyl derivatives of beta-D-glucopyranosylamine, N-acetyl-beta-D-glucopyranosylamine (1-GlcNAc), has been characterized by kinetic, ultracentrifugation, and crystallographic studies. 1-GlcNAc acts as a competitive inhibitor for both the b (Ki = 32 microM) and the a (Ki = 35 microM) forms of the enzyme with respect to glucose 1-phosphate and in synergism with caffeine, mimicking the binding of glucose. Sedimentation velocity experiments demonstrated that 1-GlcNAc was able to induce dissociation of tetrameric phosphorylase a and stabilization of the dimeric T-state conformation. Co-crystals of the phosphorylase b-1-GlcNAc-IMP complex were grown in space group P4(3)2(1)2, with native-like unit cell dimensions, and the complex structure has been refined to give a crystallographic R factor of 18.1%, for data between 8 and 2.3 A resolution. 1-GlcNAc binds tightly at the catalytic site of T-state phosphorylase b at approximately the same position as that of alpha-D-glucose. The ligand can be accommodated in the catalytic site with very little change in the protein structure and stabilizes the T-state conformation of the 280s loop by making several favorable contacts to Asn 284 of this loop. Structural comparisons show that the T-state phosphorylase b-1-GlcNAc-IMP complex structure is overall similar to the T-state phosphorylase b-alpha-D-glucose complex structure. The structure of the 1-GlcNAc complex provides a rational for the biochemical properties of the inhibitor.