Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA.
We have determined the 3.0 A resolution structure of wild-type HIV-1 reverse transcriptase in complex with an RNA:DNA oligonucleotide whose sequence includes a purine-rich segment from the HIV-1 genome called the polypurine tract (PPT). The PPT is resistant to ribonuclease H (RNase H) cleavage and is used as a primer for second DNA strand synthesis. The 'RNase H primer grip', consisting of amino acids that interact with the DNA primer strand, may contribute to RNase H catalysis and cleavage specificity. Cleavage specificity is also controlled by the width of the minor groove and the trajectory of the RNA:DNA, both of which are sequence dependent. An unusual 'unzipping' of 7 bp occurs in the adenine stretch of the PPT: an unpaired base on the template strand takes the base pairing out of register and then, following two offset base pairs, an unpaired base on the primer strand re-establishes the normal register. The structural aberration extends to the RNase H active site and may play a role in the resistance of PPT to RNase H cleavage.
Center for Advanced Biotechnology and Medicine and Rutgers University Chemistry Department, 679 Hoes Lane, Piscataway, NJ 08854-5638, USA.
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Sarafianos
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Das
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Tantillo
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Clark
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Ding
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Whitcomb
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Boyer
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Hughes
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Arnold
D003461:Crystallography; D017931:DNA Primers / Q000737:chemistry; D054303:HIV Reverse Transcriptase / Q000737:chemistry*; D015497:HIV-1 / Q000254:growth & development; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D009843:Oligoribonucleotides / Q000737:chemistry*; D011061:Poly A / Q000737:chemistry; D011071:Poly T / Q000737:chemistry; D011067:Poly dA-dT / Q000737:chemistry; D020836:Protein Structure, Quaternary; D011687:Purines / Q000737:chemistry*; D016914:Ribonuclease H / Q000737:chemistry; D013379:Substrate Specificity; D013499:Surface Properties; D017356:Synchrotrons; D014158:Transcription, Genetic; D014779:Virus Replication
D017931:DNA Primers; D009838:Oligodeoxyribonucleotides; D009843:Oligoribonucleotides; D011687:Purines; C016023:oligo(dA-dT); D011061:Poly A; D011071:Poly T; D011067:Poly dA-dT; C008950:poly A-T; D054303:HIV Reverse Transcriptase; D016914:Ribonuclease H