Regiospecificity of nucleotide-amino acid mating vs. water dynamics: a key to protein-nucleic acid assemblies: structure of unidecahydrated inosine-5'-monophosphate and L-glutamic acid (2C10H13N4O8P.C5H11NO4.11H2O) cocrystal at atomic resolution

Abstract

The crystal structure of a unidecahydrated cocomplex between two Inosine-5′-monophosphates (IMP) and one L-glutamic acid has been determined by X-ray crystallographic methods. The crystal belongs to the monoclinic space group P21 with cell dimensions a = 8.650(1), b = 21.900(1), c = 12.370(1) A, and β = 110.4°(9). This structure reveals extensive hydrogen bonding of glutamic acid to the nucleotide through direct and water-mediated interactions. The phosphate oxygens (O3B and O1B) seem to prefer nonspecific interaction with the functional sites of glutamic acid (OE2 ······O1B = 1.78 A, NA······O3B = 2.73 A, OH······O3B = 3.06 A), whereas the bases prefer specific (O······N3B = 2.88 A) binding. A solvent mediated N7A···W5···N7B hydrogen bond used for stabilization of the stacked purine bases has been observed as in other amino acid–nucleotide cocrystals. Glutamic acid occupies the same hydrophilic region in the nucleotide cocrystal as was found in glutamine–inosine monophosphate (Gln–IMP) and in serine–inosine monophosphate (Ser–IMP) complexes through substantial replacement of free and bound water molecules. This points to the dynamic hydrogen bonding nature of the water molecules and their stereochemical cooperation for the placement of amino acid through the polycoordination within the crystal.