Crystal Structure of 2A Proteinase from Hand, Foot and Mouth Disease Virus

EV71 is responsible for several epidemics worldwide; however, the effective antiviral drug is unavailable to date. The 2A proteinase (2Apro) of EV71 presents a promising drug target due to its multiple roles in virus replication, inhibition of host protein synthesis and evasion of innate immunity. We determined the crystal structure of EV71 2Apro at 1.85 Å resolution, revealing that the proteinase maintains a chymotrypsin-like fold. The active site is composed of the catalytic triads C110A, H21 and D39 with the geometry similar to that in other picornaviral 2Apro, 3Cpro and serine proteinases. The cI-to-eI2 loop at the N-terminal domain of EV71 2Apro adopts a highly stable conformation and contributes to the hydrophilic surface property, which are strikingly different in HRV2 2Apro but are similar in CVB4 2Apro. We identified a hydrophobic motif “LLWL” followed by an acidic motif “DEE” at the C-terminus of EV71 2Apro. The “LLWL” motif is folded into the β-turn structure that is essential for the positioning of the acidic motif. Our structural and mutagenesis study demonstrated that both the negative charging and the correct positioning of the C-terminus are essential for EV71 replication. Deletion of the “LLWL” motif abrogated the proteolytic activity, indicating that the motif is critical for maintaining the active proteinase conformation. Our findings provide the structural and functional insights into EV71 2Apro and establish a framework for structure-based inhibitor design.