4eq0 | pdb_00004eq0

Crystal Structure of inactive single chain variant of HIV-1 Protease in Complex with the substrate p2-NC

spinqualitylabelsall models 4eq0, resolution 1.70Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4eq0 is a 2 chain structure with sequence from Hiv-1 m:b_arv2/sf2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ACT, BME, EDO, GOL, PO4 Related: 4ep2, 4ep3, 4epj, 4eqj Gene: gag-pol (HIV-1 M:B_ARV2/SF2) Activity: HIV-1 retropepsin, with EC number 3.4.23.16 Resources: FirstGlance, OCA, RCSB, PDBsum Publication Abstract from PubMed HIV-1 protease recognizes and cleaves more than 12 different substrates leading to viral maturation. While these substrates share no conserved motif, they are specifically selected for and cleaved by protease during viral life cycle. Drug resistant mutations evolve within the protease that compromise inhibitor binding but allow the continued recognition of all these substrates. While the substrate envelope defines a general shape for substrate recognition, successfully predicting the determinants of substrate binding specificity would provide additional insights into the mechanism of altered molecular recognition in resistant proteases. We designed a variant of HIV protease with altered specificity using positive computational design methods and validated the design using x-ray crystallography and enzyme biochemistry. The engineered variant, Pr3 (A28S/D30F/G48R), was designed to preferentially bind to one out of three of HIV protease's natural substrates; RT-RH over p2-NC and CA-p2. In kinetic assays, RT-RH binding specificity for Pr3 increased three-fold compared to the wild-type (WT), which was further confirmed by isothermal titration calorimetry. Crystal structures of WT protease and the designed variant in complex with RT-RH, CA-p2 and p2-NC were determined. Structural analysis of the designed complexes revealed that one of the engineered substitutions (G48R) potentially stabilized heterogeneous flap conformations, thereby facilitating alternate modes of substrate binding. Our results demonstrate that while substrate specificity could be engineered in HIV protease, the structural pliability of protease restricted the propagation of interactions as predicted. These results offer new insights into the plasticity and structural determinants of substrate binding specificity of the HIV-1 protease. Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease.,Alvizo O, Mittal S, Mayo SL, Schiffer CA Protein Sci. 2012 May 1. doi: 10.1002/pro.2086. PMID:22549928 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Virus protease

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