Crystallization and preliminary X-ray crystallographic analysis of malonamidase E2, an amidase signature family member

Abstract

Malonamidase E2 from Bradyrhizobium japonicum catalyzes the hydrolysis of malonamate. The enzyme belongs to an amidase signature family which has a highly conserved serine- and glycine-rich sequence over a stretch of approximately 45 amino acids. More than 100 known or predicted members belonging to this family, whose biological functions vary widely, can be identified in sequence databases. Although urgently needed, no three-dimensional structure of any protein of this family is yet available. The crystallization of malonamidase E2 was undertaken as a first step toward the goal of providing information on the canonical structure of the amidase signature family. The enzyme was crystallized using the hanging-drop vapour-diffusion method at 277 K under two different conditions. One crystal form, which is easier to work with than the other form, belongs to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 104.29, b = 95.58, c = 74.90 A. The unit cell is likely to contain two molecules of MAE2, with a crystal volume per protein mass (V(M)) of 2.045 A(3)Da(-1) and solvent content of about 39.9% by volume. A native data set to 1.8 A resolution was obtained from a flash-cooled crystal using synchrotron radiation.