Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor

Human immunodeficiency virus 1 (HIV-1) infection is a global health issue since neither a cure nor a vaccine is available. However, the highly active antiretroviral therapy (HAART) has improved the life expectancy for patients with acquired immunodeficiency syndrome (AIDS). Nucleoside reverse transcriptase inhibitors (NRTIs) are in almost all HAART and target reverse transcriptase (RT), an essential enzyme for the virus. Even though NRTIs are highly effective, they have limitations caused by RT resistance. The main mechanisms of RT resistance to NRTIs are discrimination and excision. Understanding the molecular mechanisms for discrimination and excision are essential to develop more potent and selective NRTIs. Using protein X-ray crystallography, we determined the first crystal structure of RT in its post-catalytic state in complex with emtricitabine, (-)FTC or stavudine (d4T). Our structural studies provide the framework for understanding how RT discriminates between NRTIs and natural nucleotides, and for understanding the requirement of (-)FTC to undergo a conformation change for successful incorporation by RT. The crystal structure of RT in post-catalytic complex with d4T provides a “snapshot” for considering the possible mechanism of how RT develops resistance for d4T via excision. The findings reported herein will contribute to the development of next generation NRTIs.

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Crystal structure of prototype foamy virus (PFV) protease-reverse transcriptase fusion (PR-RT) reveals conformational plasticity: implications for function

10.1101/2020.11.23.395087 ◽

2020 ◽

Author(s):

Jerry Joe E. K. Harrison ◽

Steve Tuske ◽

Kalyan Das ◽

Francesc X. Ruiz ◽

Joseph D. Bauman ◽

...

Keyword(s):

Crystal Structure ◽

Reverse Transcriptase ◽

Foamy Virus ◽

Rnase H ◽

Proteolytic Processing ◽

Nucleic Acid Binding ◽

Foamy Viruses ◽

Conformational Plasticity ◽

Polyprotein Precursor ◽

Hiv 1

AbstractProteolytic processing of the retroviral Pol polyprotein precursor produces protease (PR), reverse transcriptase (RT), and integrase (IN), except in foamy viruses (FVs) where only the IN domain is released. Here, we report the 2.9 Å resolution crystal structure of the mature PR-RT from prototype FV (PFV) needed for processing and reverse transcription. The monomeric PFV PR exhibits similar architecture as the HIV-1 PR but the N- and C-terminal residues are unstructured. A C-terminal extension of the PR folds into two helices that supports the RT palm subdomain and anchors the PR next to the RT. The subdomains of RT: fingers, palm, thumb, and connection, and the RNase H domain, are connected by flexible linkers and spatially arranged similarly to those in the HIV-1 RT p51 subunit. Significant spatial and conformational domain rearrangements are required for nucleic acid binding. This offers structural insight into retroviral RT conformational maturation and architecture of immature enzymes.

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