E. coli 5′-nucleotidase undergoes a hinge-bending domain rotation resembling a ball-and-socket motion

Structures of nine independent conformers of E. coli 5′-nucleotidase (5′-NT) have been analyzed using four different crystal forms. These data show that the two-domain protein undergoes an unusual 96° hinge-bending domain rotation. Structures of the open and closed forms with substrates and inhibitors reveal that the substrate moves by ∼25 Å with the large domain rotation into the catalytic site. The domain motions derived from a comparison of the nine conformations agree well with motions obtained from a normal mode analysis in that all independent domain rotations are around axes that are roughly located in the plane which includes the domain centers and the hinge. Two residues, Lys355 and Gly356, form the core of the hinge region and undergo a large change of the main-chain torsion angles. The hinge-bending movement observed for 5′-nucleotidase differs markedly from a classical hinge-bending closure motion which involves an opening of the substrate or ligand-binding cleft between two domains. In contrast, the movement observed in 5′-nucleotidase resembles that of a ball-and-socket joint. The smaller C-terminal domain rotates approximately around its center such that the residues at the domain interface move in a sliding motion along the interface. Few direct interdomain contacts and a layer of water molecules between the two domains facilitate the sliding motion.