Crystal structure of adenylosuccinate synthetase from Escherichia coli. Evidence for convergent evolution of GTP-binding domains

Abstract

The structure of the P2(1) crystal form of adenylosuccinate synthetase from Escherichia coli has been determined to a resolution of 2.8 A. The refined model for the enzyme gives an R factor of 0.20 and a root-mean-square deviation from expected bond lengths and angles of 0.016 A and 2.27 degrees, respectively. The dominant structural element of each monomer of the homodimer is a central beta-sheet of 10 strands. The first nine strands of the sheet are mutually parallel with right-handed crossover connections between the strands. The 10th strand is antiparallel with respect to the first nine strands. In addition, the enzyme has two antiparallel beta-sheets, comprised of two strands and three strands each, 11 alpha-helices and two short 3/10-helices. The overall fold of the polypeptide chain has not been observed heretofore in any other protein structure. Residues tentatively assigned to the active site of the enzyme on the basis of chemical modification and directed mutation cluster in two separate regions. Gly12, Gly15, Gly17, Lys18, Ile19, and Lys331 lie at one end of a crevice that measures 12 A by 30 A by 12 A deep. Lys140 and Arg147 are not part of this crevice, but instead lie at the interface between monomers of the dimer. Lys140 makes a salt link with Asp231 of a monomer related by molecular symmetry and Arg147 binds to the carbonyl of the same Asp231. Superposition of the p21 ras protein (Pai, E. F., Kabsch, W., Krengel, U., Holmes, K., John, J., and Wittinghofer, A. (1989) Nature 341, 209-214) onto the synthetase reveals significant correspondences between side chains of the two proteins. Residues which interact with GTP in the p21ras protein have structurally equivalent residues in the synthetase. The GTP molecule, when transformed to the coordinate frame of the synthetase, falls into the crevice defined by studies in directed mutation. We suggest that the similarities in the GTP-binding domains of the synthetase and the p21ras protein are an example of convergent evolution of two distinct families of GTP-binding proteins.