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The structure of unliganded reverse transcriptase from the human immunodeficiency virus type 1
D W Rodgers1, S J Gamblin, B A Harris
1Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138.
Summary
Structural analysis of HIV-1 reverse transcriptase reveals significant domain shifts upon Nevirapine binding. These rearrangements, particularly in the thumb domain, may hinder substrate binding and impact enzyme function.
Area of Science:
- Structural Biology
- Virology
- Biochemistry
Background:
- Human Immunodeficiency Virus type 1 (HIV-1) reverse transcriptase (RT) is a crucial enzyme for viral replication.
- Understanding the structural dynamics of RT is essential for developing effective antiviral therapies.
Purpose of the Study:
- To determine the crystal structure of HIV-1 RT.
- To compare the unliganded RT structure with complexes bound to a polymerase inhibitor (Nevirapine) and an oligonucleotide.
Main Methods:
- X-ray crystallography was used to determine the structure of HIV-1 RT at 3.2-A resolution.
- Comparative structural analysis was performed on the unliganded enzyme and its complexes.
Main Results:
- The HIV-1 RT structure reveals a heterodimer (p66/p51) with distinct functional domains.
- Significant conformational changes, including a ~33-degree rotation of the p66 thumb domain, were observed upon Nevirapine binding.
- Nevirapine binds to the p66 palm domain, inducing a local rearrangement of a beta-sheet.
- No rearrangements were observed within the polymerase active site itself between RT and the RT/DNA complex.
Conclusions:
- Ligand binding, particularly to Nevirapine, induces substantial domain rearrangements in HIV-1 RT.
- These structural changes may allosterically affect substrate binding and enzyme activity.
- The findings provide insights into the mechanism of non-nucleoside reverse transcriptase inhibitor action.