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Crystal structure of HIV‐1 reverse transcriptase in complex with a polypurine tract RNA:DNA
Author(s) -
Sarafianos Stefan G.,
Das Kalyan,
Tantillo Chris,
Clark Arthur D.,
Ding Jianping,
Whitcomb Jeannette M.,
Boyer Paul L.,
Hughes Stephen H.,
Arnold Edward
Publication year - 2001
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1093/emboj/20.6.1449
Subject(s) - rnase h , reverse transcriptase , biology , base pair , dna , primer (cosmetics) , rna , oligonucleotide , rnase p , microbiology and biotechnology , cleavage (geology) , genetics , gene , chemistry , paleontology , organic chemistry , fracture (geology)
We have determined the 3.0 Å 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.