Open structures of MurD: Domain movements and structural similarities with folylpolyglutamate synthetase

UDP-N-acetylmuramoyl-L-alanine:D-glutamate (MurD) ligase catalyses the addition of D-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). The crystal structures of Escherichia coli in the substrate-free form and MurD complexed with UMA have been determined at 2.4 Angstrom and 1.88 Angstrom resolution, respectively. The MurD structure comprises three domains each of a topology reminiscent of nucleotide-binding folds. In the two structures the C-terminal domain undergoes a large rigid-body rotation away from the N-terminal and central domains. These two open structures were compared with the four published closed structures of MurD. In addition the comparison reveals which regions are affected by the binding of UMA, ATP and D-Glu. Also we compare and discuss two structurally characterized enzymes which belong to the same ligase superfamily: MurD and folylpolyglutamate synthetase (FGS). The analysis allows the identification of key residues involved in the reaction mechanism of FGS. The determination of the two open conformation structures represents a new step towards the complete elucidation of the enzymatic mechanism of the MurD ligase. (C) 2000 Academic Press.