398D

3'-DNA-RNA-5' JUNCTION FORMED DURING INITIATION OF MINUS-STRAND SYNTHESIS OF HIV REPLICATION

Summary for 398D

• Entry DOI: 10.2210/pdb398d/pdb
• Descriptor: RNA (5'-R(*GP*CP*AP*GP*UP*GP*GP*C)-3'), DNA/RNA (5'-R(*GP*CP*CP*AP)-D(*CP*TP*GP*C)-3') (3 entities in total)
• Functional Keywords: a-dna/rna, double helix, dna-rna hybrid
• Total number of polymer chains: 4
• Total formula weight: 10066.36

Authors

Mueller, U.,Meier, G.,Mochi-Onori, A.,Cellai, L.,Heumann, H. (deposition date: 1998-05-04, release date: 1998-10-06, Last modification date: 2024-04-03)

Primary citation

Mueller, U.,Maier, G.,Mochi Onori, A.,Cellai, L.,Heumann, H.,Heinemann, U.
Crystal structure of an eight-base pair duplex containing the 3'-DNA-RNA-5' junction formed during initiation of minus-strand synthesis of HIV replication.
Biochemistry, 37:12005-12011, 1998

PubMed Abstract: During initiation of minus-strand synthesis by HIV-1 reverse transcriptase, a 3'-DNA-RNA-5' junction is formed involving the 3'-end of tRNAlys,3. The HIV-RT-associated RNase H cleaves the RNA template strand specifically, opposite the newly synthesized DNA strand. We have determined the crystal structure at 1.9 A resolution of an eight-base pair hybrid duplex representing the junction to identify global or local structural perturbations which may be recognized by HIV-RT RNase H. The junction octamer is in a global A-type conformation throughout. A base pair step with distinct stacking geometry and variable backbone conformation is located next to the main endonucleolytic cleavage site. This base pair step may serve as a recognition site for HIV-RT RNase H.

PubMed: 9724510
DOI: 10.1021/bi981152y

Experimental method

X-RAY DIFFRACTION (1.94 Å)