HIV-1 Reverse Transcriptase in Complex with Nevirapine: Difference between revisions
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<StructureSection load='3v81' size='350' side='right' caption='Crystal Structure of HIV-1 Reverse Transcriptase with DNA and the nonnucleoside inhibitor nevirapine (PDB entry [[3V81]])' scene=''> | <StructureSection load='3v81' size='350' side='right' caption='Crystal Structure of HIV-1 Reverse Transcriptase with DNA and the nonnucleoside inhibitor nevirapine (PDB entry [[3V81]])' scene=''> | ||
== Structure of RT domains == | == Structure of RT domains == | ||
RT is an asymmetric heterodimer composed of a 560 amino acid 66kDa subunit (p66) and a 440 amino acid 51kDa subunit (p51). The p66 and p55 domains are derived from cleavage of the same polyprotein precursor. The p51 is made from the C-terminal cleavage of the p66 subunit by HIV-1 protease. As a result, they share a common amino terminus, but the p51 subunit does not have an RNase H domain. | RT is an asymmetric heterodimer composed of a 560 amino acid 66kDa subunit (p66) and a 440 amino acid 51kDa subunit (p51). The p66 and p55 domains are derived from cleavage of the same polyprotein precursor. The p51 is made from the C-terminal cleavage of the p66 subunit by HIV-1 protease. As a result, they share a common amino terminus, but the p51 subunit does not have an RNase H domain. | ||
The p66 subunit contains two enzymatically active domains, polymerase (color)and RNase H (color). This polymerase is responsible for catalyzing the polymerization of DNA using either RNA or DNA as the template. The endonucleolytic ribonuclease H (RNase H) specifically degrades the RNA strand of RNA:DNA duplexes that are produced during retrotranscription. RT has a right-hand structure.<ref>PMID:10364165<ref/> The polymerase domain can be divided into several subdomains: the fingers (residues 1-85 and 118-155), palm (residues 86-117 and 156-236), thumb (237-318) and connecting (319-426). The RNase H domain consists of the C-terminal residues 427-560. | The p66 subunit contains two enzymatically active domains, polymerase (color)and RNase H (color). This polymerase is responsible for catalyzing the polymerization of DNA using either RNA or DNA as the template. There are three asp residues (D110, D185, D186) in polymerase's active site that play a key role in the enzyme's function and are referred to as the <scene name='HIV-1_Reverse_Transcriptase_in_Complex_with_Nevirapine/Pol_active_site_residues/2'>catalytic residues</scene>. The endonucleolytic ribonuclease H (RNase H) specifically degrades the RNA strand of RNA:DNA duplexes that are produced during retrotranscription. RT has a right-hand structure.<ref>PMID:10364165<ref/> The polymerase domain can be divided into several subdomains: the fingers (residues 1-85 and 118-155), palm (residues 86-117 and 156-236), thumb (237-318) and connecting (319-426). The RNase H domain consists of the C-terminal residues 427-560. | ||
The p51 subunit contains the same four subdomains as the polymerase domain in p66, but in different positions. The p51 subunit is therefore non-enzymatic, and instead stabilizes the proper folding of the catalytic p66 subunit. Instead of adopting an "open" catalytically-active conformation that can accommodate a nucleic acid template strand like p66, the p51 subunit is in a "closed" conformation and plays a largely structural role.<ref>PMID:1377403</ref> | The p51 subunit contains the same four subdomains as the polymerase domain in p66, but in different positions. The p51 subunit is therefore non-enzymatic, and instead stabilizes the proper folding of the catalytic p66 subunit. Instead of adopting an "open" catalytically-active conformation that can accommodate a nucleic acid template strand like p66, the p51 subunit is in a "closed" conformation and plays a largely structural role.<ref>PMID:1377403</ref> | ||
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== The NNRTI Binding Pocket == | == The NNRTI Binding Pocket == | ||
Although nonnucleoside RT inhibitors are structurally diverse compounds, they all bind RT in the same location - <scene name='HIV-1_Reverse_Transcriptase_in_Complex_with_Nevirapine/Nnrti_binding_pocket/2'>the NNRTI hydrophobic binding pocket</scene>. The pocket is located in the palm domain of the p66 subunit between the β6-β10-β9 and β12-β13-β14 sheets approximately 10 angstroms from the three catalytic asp residues that make up the polymerase active site.<ref>PMID:1377403</ref> The NNRTI BP is mostly hydrophobic in nature with considerable aromatic residues (Y181, Y188, F227, W229, and Y232), but also contains several hydrophilic residues (K101, K103, S105, D192, and E224 of the p66 subunit and E138 of the β7-β8 loop of the p51 subunit). NNRTIs most likely access the binding pocket at the p66/p51 heterodimer interface surrounded by residues L100, K101, K103, V179, and Y181 of the p66 subunit and E138 of the p51 subunit. These residues are colored tan in the binding pocket scene. <ref>PMID:8805568</ref> Actually, in the absence of ligand, the side chains of Y181 and Y188 point into the core, so the binding pocket doesn't exist in the free enzyme. The binding of NNRTI to HIV RT causes these side chains to shift away and make room for the ligand to enter the binding pocket.<ref>PMID:8805568</ref> | Although nonnucleoside RT inhibitors are structurally diverse compounds, they all bind RT in the same location - <scene name='HIV-1_Reverse_Transcriptase_in_Complex_with_Nevirapine/Nnrti_binding_pocket/2'>the NNRTI hydrophobic binding pocket</scene>. The pocket is located in the palm domain of the p66 subunit between the β6-β10-β9 and β12-β13-β14 sheets approximately 10 angstroms from the three catalytic asp residues that make up the polymerase active site.<ref>PMID:1377403</ref> The NNRTI BP is mostly hydrophobic in nature with considerable aromatic residues (Y181, Y188, F227, W229, and Y232), but also contains several hydrophilic residues (K101, K103, S105, D192, and E224 of the p66 subunit and E138 of the β7-β8 loop of the p51 subunit). NNRTIs most likely access the binding pocket at the p66/p51 heterodimer interface surrounded by residues L100, K101, K103, V179, and Y181 of the p66 subunit and E138 of the p51 subunit. These residues are colored tan in the binding pocket scene. <ref>PMID:8805568</ref> Actually, in the absence of ligand, the side chains of <scene name='HIV-1_Reverse_Transcriptase_in_Complex_with_Nevirapine/Y181_and_y188/2'>Y181 and Y188</scene> point into the core, so the binding pocket doesn't exist in the free enzyme. The binding of NNRTI to HIV RT causes these side chains to shift away and make room for the ligand to enter the binding pocket.<ref>PMID:8805568</ref> | ||
== Effects of nevirapine binding on RT-DNA complex == | == Effects of nevirapine binding on RT-DNA complex == | ||
