Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA

Sarafianos, Stefan G.; Das, Kalyan; Tantillo, Chris; Clark Jr, Arthur D.; Ding, Jianping; Whitcomb, Jeannette M.; Boyer, Paul L.; Hughes, Stephen H.; Arnold, Edward
March 2001
EMBO Journal;3/15/2001, Vol. 20 Issue 6, p1449
Academic Journal
We have determined the 3.0 Ã… 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.


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