A structural study of TatD from elucidates a putative DNA-binding mode of a Mg-dependent nuclease.

TatD has been thoroughly investigated as a DNA-repair enzyme and an apoptotic nuclease, and still-unknown TatD-related DNases are considered to play crucial cellular roles. However, studies of TatD from Gram-positive bacteria have been hindered by an absence of atomic detail and the resulting inability to determine function from structure. In this study, an X-ray crystal structure of SAV0491, which is the TatD enzyme from the Gram-positive bacterium (TatD), is reported at a high resolution of 1.85 Å with a detailed atomic description. Although TatD has the common TIM-barrel fold shared by most TatD-related homologs, and PDB entry 2gzx shares 100% sequence identity with SAV0491, the crystal structure of TatD revealed a unique binding mode of two phosphates interacting with two Ni ions. Through a functional study, it was verified that TatD has Mg-dependent nuclease activity as a DNase and an RNase. In addition, structural comparison with TatD homologs and the identification of key residues contributing to the binding mode of Ni ions and phosphates allowed mutational studies to be performed that revealed the catalytic mechanism of TatD. Among the key residues composing the active site, the acidic residues Glu92 and Glu202 had a critical impact on catalysis by TatD. Furthermore, based on the binding mode of the two phosphates and structural insights, a putative DNA-binding mode of TatD was proposed using docking. Overall, these findings may serve as a good basis for understanding the relationship between the structure and function of TatD proteins from Gram-positive bacteria and may provide critical insights into the DNA-binding mode of TatD.