Structure of D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor carrying the fluorescent NAD derivatives at 2.7 A resolution.

Ultraviolet irradiation of carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase leads to the formation of a fluorescent NAD derivative. The structure of the enzyme from Palinurus versicolor carrying this derivative has been determined by molecular replacement and refined using the restrained least-squares method to 2.7 A with a final crystallographic R-factor of 0.205. The polypeptide chain folding and subunit arrangement closely resemble the known structure of Homarus americanus GAPDH. The structure at the modified active site confirms that the photochemical reaction is a half-of-the-sites reaction and occurs in the red and yellow subunit pair. The stereochemical relationship between the Trp residues at the active site shows that Trp 310 is most probably involved in a radiationless energy transfer to the fluorophore. A large solvent channel connecting the catalytic and NAD(+)-binding sites was found parallel to the crystallographic axis alpha from packing analysis, suggesting that this crystal form may be suitable for a kinetic crystallographic study of the apoenzyme.