Structure of apo-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor

D-Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) shows cooperative proper ties for binding coenzymes. The structure of apo-GAPDH from Palinurus versi color has been solved at 2.0 Angstrom resolution by X-ray crystallography. The final model gives a crystallographic R factor of 0.178 in the resolutio n range 8 to 2 Angstrom. The structural comparison with holo-GAPDN from the same species reveals a conformational change induced by coenzyme binding s imilar to that observed in Bacillus stearothermophilus GAPDH but to a lesse r extent. The differences in magnitude during the apo-holo transition betwe en these two enzymes were analyzed with respect to the change of the amino acid composition in the coenzyme binding pocket. In the crystalline state o f apo-GAPDH, the overall structures of the subunits are similar to each oth er; however, significant differences in temperature factors and minor diffe rences in domain rotation upon coenzyme binding were observed for different subunits. These structural features are discussed in relation to the envir onmental asymmetry of crystallographically independent subunits. (C) 2000 A cademic Press.