1HYS

CRYSTAL STRUCTURE OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH A POLYPURINE TRACT RNA:DNA

Summary for 1HYS

• Entry DOI: 10.2210/pdb1hys/pdb
• Related: 1DLO 1RTD 2HMI
• Descriptor: 5'-R(*UP*CP*AP*GP*CP*CP*AP*CP*UP*UP*UP*UP*UP*AP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3', 5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*AP*AP*AP*AP*AP*GP*TP*GP*GP*CP*TP*G)-3', HIV-1 REVERSE TRANSCRIPTASE, ... (6 entities in total)
• Functional Keywords: polypurine tract, ppt, protein-nucleic acid complex, rnase h, rna:dna, unpaired base, rnase h primer grip, transferase-dna-rna complex, transferase-dna-rna hybrid complex, transferase/dna-rna hybrid
• Biological source: Human immunodeficiency virus 1; More
• Cellular location: Matrix protein p17: Virion (Potential). Capsid protein p24: Virion (Potential). Nucleocapsid protein p7: Virion (Potential). Reverse transcriptase/ribonuclease H: Virion (Potential). Integrase: Virion (Potential): P03366 P03366
• Total number of polymer chains: 6
• Total formula weight: 173779.96

Authors

Sarafianos, S.G.,Das, K.,Tantillo, C.,Clark Jr., A.D.,Ding, J.,Whitcomb, J.,Boyer, P.L.,Hughes, S.H.,Arnold, E. (deposition date: 2001-01-22, release date: 2001-03-26, Last modification date: 2024-10-30)

Primary citation

Sarafianos, S.G.,Das, K.,Tantillo, C.,Clark Jr., A.D.,Ding, J.,Whitcomb, J.M.,Boyer, P.L.,Hughes, S.H.,Arnold, E.
Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA.
EMBO J., 20:1449-1461, 2001

PubMed Abstract: 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.

PubMed: 11250910
DOI: 10.1093/emboj/20.6.1449

Experimental method

X-RAY DIFFRACTION (3 Å)