Structure of HIV-1 reverse transcriptase cleaving RNA in an RNA/DNA hybrid

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 115; no. 3; pp. 507 - 512
• Main Authors: Tian, Lan, Kim, Min-Sung, Li, Hongzhi, Wang, Jimin, Yang, Wei
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 16.01.2018
• Subjects: BASIC BIOLOGICAL SCIENCES; Biological Sciences; Catalytic Domain; Conformation; connection domain; Crystallography, X-Ray; Deoxyribonucleic acid; DNA; DNA polymerase; DNA, Viral - chemistry; DNA, Viral - genetics; DNA, Viral - metabolism; DNA-directed DNA polymerase; Drug screening; HIV; HIV Infections - virology; HIV Reverse Transcriptase - chemistry; HIV Reverse Transcriptase - genetics; HIV Reverse Transcriptase - metabolism; HIV-1 - chemistry; HIV-1 - enzymology; HIV-1 - genetics; Homology; Human immunodeficiency virus; Humans; Hybridization; minor groove recognition; Models, Molecular; Nuclease; Nucleic Acid Conformation; Nucleotide sequence; Nucleotides; Phosphates; polypurine tract; Ribonuclease H; Ribonuclease H - chemistry; Ribonuclease H - genetics; Ribonuclease H - metabolism; Ribonucleic acid; RNA; RNA, Viral - chemistry; RNA, Viral - genetics; RNA, Viral - metabolism; RNA-directed DNA polymerase; RNase H; sequence specificity; Substrate Specificity; Substrates; RNase H; sequence specificity; polypurine tract; minor groove recognition; connection domain
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1719746115

HIV-1 reverse transcriptase (RT) contains both DNA polymerase and RNase H activities to convert the viral genomic RNA to dsDNA in infected host cells. Here we report the 2.65-Å resolution structure of HIV-1 RT engaging in cleaving RNA in an RNA/DNA hybrid. A preferred substrate sequence is absolutely required to enable the RNA/DNA hybrid to adopt the distorted conformation needed to interact properly with the RNase H active site in RT. Substituting two nucleotides 4 bp upstream from the cleavage site results in scissile-phosphate displacement by 4 Å. We also have determined the structure of HIV-1 RT complexed with an RNase H-resistant polypurine tract sequence, which adopts a rigid structure and is accommodated outside of the nuclease active site. Based on this newly gained structural information and a virtual drug screen, we have identified an inhibitor specific for the viral RNase H but not for its cellular homologs.