Fig. 1: The crystal structure, active site and hypothesized catalytic mechanism of snake venom phosphodiesterase (VPD).

A The crystal structure of VPD shows the enzyme consists of three structural domains, i.e. the N-term (blue), PDE (palecyan) and NUC (orange) domains. The active site is located in the PDE domain and contains two Zn²⁺ ions, PDB code: 5GZ5. B The binding site of VPD accommodating dTMP nucleotide is depicted by molecular surface (left) and cartoon models. Zn²⁺ ions are shown as spheres with labels. The N and S pockets for nucleotides are indicated. Crucial amino acid residues are colored differently in the surface model and shown as sticks in the cartoon model. C The two-step inline displacement mechanism proposed for the enzymatic hydrolysis of phosphodiester by PDEs. The R³’ represents the 3’-terminal nucleotide, while R is the second nucleotide counted from the 3’-end. Threonine (T185) acts as a nucleophile attacking the phosphorus to form a trigonal bipyramidal transition state. The Oγ atom of T185, phosphorus and the oxygen connecting to R are supposed to be aligned in a line as indicated by the blue arc arrows.