Article
- The EMBO Journal (2001) 20, 1449 - 1461
- doi:10.1093/emboj/20.6.1449
Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA
Stefan G. Sarafianos1, Kalyan Das1, Chris Tantillo1, Arthur D. Clark Jr1, Jianping Ding1, Jeannette M. Whitcomb2, Paul L. Boyer3, Stephen H. Hughes3 and Edward Arnold1
- Center for Advanced Biotechnology and Medicine (CABM) and Rutgers University Chemistry Department, 679 Hoes Lane, Piscataway, NJ 08854-5638, USA
- ViroLogic, Inc., 270 E. Grand Avenue, S. San Francisco, CA 94080, USA
- HIV Drug Resistance Program, NCI-Frederick Cancer Research and Development Center, PO Box B, Frederick, MD 21702-1201, USA
Correspondence to:
Edward Arnold, E-mail: arnold@cabm.rutgers.edu
Received 1 December 2000; Accepted 30 January 2001; Revised 25 January 2001
Abstract
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.
Keywords:
- HIV-1,
- polypurine tract,
- reverse transcriptase,
- RNase H,
- RNA:DNA
