Crystal Packing of Protomers Provides a Valuable Structural Insight into Protein Structure

The crystal structure of proteins is generally considered static due to the constraints imposed by crystal packing. We determined the crystal structure of rice NADP-malic enzyme 2 (OsNADP-ME2), an oxidative decarboxylase that converts malic acid to pyruvate and provides NADPH to generate reactive oxygen species. The OsNADP-ME2 is crystallized as a tetramer in the space group of P21. In the crystal, all the crystal packing interactions are made through the NADP-binding domain of the enzyme. Interestingly, a protomer shows a conformational change, with a 7.4° tilt in the NADP-binding domain. Basically, the crystal packing consists of a horizontal arrangement of vertically parallel P21 screw axes. In the vertical direction, a protomer (Mol A) is tightly sandwiched by two protomers (Mol C) of nearby tetramers and vice versa. In the horizontal direction, two protomers (Mol B and D) of a tetramer are parallelly bound to nearby tetramers, of which one protomer (Mol B) has tighter interactions than the other protomer (Mol D). The protomer Mol D, with the least interaction surface in the crystal packing, adopts an open conformation of the NADP-binding domain, which may be the flexible part of the enzyme for NADP+ cofactor binding. Crystallization can provide valuable information for protein structure.