7N6T

Crystal structure of inhibitor-free HIV-1 PRS17 revertant mutant PRS17 V48G

Summary for 7N6T

• Entry DOI: 10.2210/pdb7n6t/pdb
• Related: 5T2E 5T2Z 6O54 6O57 6O5A 6O5X
• Descriptor: Protease (2 entities in total)
• Functional Keywords: hiv-1 protease, drug resistance, prs17, hydrolase
• Biological source: Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI) (HIV-1)
• Total number of polymer chains: 2
• Total formula weight: 21501.13

Authors

Burnaman, S.H.,Wang, Y.-F.,Weber, I.T. (deposition date: 2021-06-09, release date: 2021-09-08, Last modification date: 2023-10-18)

Primary citation

Burnaman, S.H.,Kneller, D.W.,Wang, Y.F.,Kovalevsky, A.,Weber, I.T.
Revertant mutation V48G alters conformational dynamics of highly drug resistant HIV protease PRS17.
J.Mol.Graph.Model., 108:108005-108005, 2021

PubMed Abstract: Drug resistance is a serious problem for controlling the HIV/AIDS pandemic. Current antiviral drugs show several orders of magnitude worse inhibition of highly resistant clinical variant PRS17 of HIV-1 protease compared with wild-type protease. We have analyzed the effects of a common resistance mutation G48V in the flexible flaps of the protease by assessing the revertant PRS17 for changes in enzyme kinetics, inhibition, structure, and dynamics. Both PRS17 and the revertant showed about 10-fold poorer catalytic efficiency than wild-type enzyme (0.55 and 0.39 μMmin compared to 6.3 μMmin). Clinical inhibitors, amprenavir and darunavir, showed 2-fold and 8-fold better inhibition, respectively, of the revertant than of PRS17, although the inhibition constants for PRS17 were still 25 to 1,200-fold worse than for wild-type protease. Crystal structures of inhibitor-free revertant and amprenavir complexes with revertant and PRS17 were solved at 1.3-1.5 Å resolution. The amprenavir complexes of PRS17 and PRS17 showed no significant differences in the interactions with inhibitor, although changes were observed in the conformation of Phe53 and the interactions of the flaps. The inhibitor-free structure of the revertant showed flaps in an open conformation, however, the flap tips do not have the unusual curled conformation seen in inhibitor-free PRS17. Molecular dynamics simulations were run for 1 μs on the two inhibitor-free mutants and wild-type protease. PRS17 exhibited higher conformational fluctuations than the revertant, while the wild-type protease adopted the closed conformation and showed the least variation. The second half of the simulations captured the transition of the flaps of PRS17 from a closed to a semi-open state, whereas the flaps of PRS17 tucked into the active site and the wild-type protease retained the closed conformation. These results suggest that mutation G48V contributes to drug resistance by altering the conformational dynamics of the flaps.

PubMed: 34419931
DOI: 10.1016/j.jmgm.2021.108005

Experimental method

X-RAY DIFFRACTION (1.32 Å)