X-ray Structure of in-situ HIV-1 protease-product complex: observation of a LBHB between catalytic aspartates

Solid State Physics Division, Bhabha Atomic Research Centre* National Institute for Rsearch in Reproductive Health, India** Institut de Biologie Structurale, France***
â—‹Madhusoodan V Hosur* Amit Das* Vishal Prashar* Smita Mahale** Laurence Serre*** Jean-Luc Ferrer***

We report here the structure of an in-situ complex between HIV-1 protease and the oligopeptide substrate AETF*YVDGAA, which corresponds to the RT-RH junction in the viral polyprotein. The structure refined to 1.65A resolution against synchrotron data, shows occurrence of the cleavage reaction in the crystal, with the two product peptides still bound in the active site before complete separation. Therefore interactions at the catalytic centre could give an insight into reaction mechanism. Both oxygens of the generated carboxyl group form hydrogen bonds : one to OD2 atom of a catalytic aspartate, and the other to the scissile nitrogen atom. The latter hydrogen bond may indicate protonation of scissile nitrogen by gem-diol hydroxyl. The inner oxygen atoms of the catalytic aspartates in the complex are 2.35Å apart indicating a LBHB. This observation of an LBHB provides the first structural support to the mechanism proposed by Northrop( Acc. Chem. Res. 2001, 34, 790 - 797), which itself is supposed to have resolved decades old uncertainties about aspartyl proteases. Further, atomic configuration of the products may be helpful for the design of mechanism-based inhibitors.