NS5B: Difference between revisions

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<scene name='NS5B/Native_ns5b/6'>Beta-hairpin in thumb domain</scene> that is proposed to move upon formation of exiting double stranded RNA.

<applet load='2HAI_DNA5.pdb' size='400' frame='true' align='left' caption='Figure 2. PDB IDs 2HAI (protein) 1RTD (DNA)' />~~Here~~ is a model of NS5B with B form DNA from HIV Reverse Transcriptase co-crystal model. DNA was modeled into the NS5B model by aligning of palms domain of NS5B and HIV reverse transcriptase in complex with DNA and an incoming dTTP then removing the HIV RT protein model while leaving the DNA where it fell into the proposed NS5B binding cleft. The catalytic Mg2+ ions are modeled in green, these would be coordinated by the three aspartic acid carboxylates, (D220, D318 and D319). A beta hairpin (residues 440-455) in the thumb domain has been moved to accommodate DNA, the hairpin is modeled into the minor groove, a possible binding site.

<applet load='2HAI_DNA5.pdb' size='400' frame='true' align='left' caption='Figure 2. PDB IDs 2HAI (protein) 1RTD (DNA)' />Figure 2 is a model of NS5B with B form DNA from HIV Reverse Transcriptase co-crystal model. DNA was modeled into the NS5B model by aligning of palms domain of NS5B and HIV reverse transcriptase in complex with DNA and an incoming dTTP then removing the HIV RT protein model while leaving the DNA where it fell into the proposed NS5B binding cleft. The catalytic Mg2+ ions are modeled in green, these would be coordinated by the three aspartic acid carboxylates, (D220, D318 and D319). A beta hairpin (residues 440-455) in the thumb domain has been moved to accommodate DNA, the hairpin is modeled into the minor groove, a possible binding site.

The template strand is seen entering through a gap in the fingers domain. An incoming dTTP that would extend the primer strand lines up with the NS5B active site and duplex DNA exits the enzyme through the large central hole. <scene name='NS5B/Ns5b_with_dna/1'>Active site</scene> <scene name='NS5B/Ns5b_with_dna/2'>Beta-hairpin</scene> P

<applet load='2HAI_catalytic3.pdb' size='400' frame='true' align='right' caption='Figure 3.' /> <scene name='NS5B/Ns5b_rna_interactions/1'>NS5B RNA interactions</scene>

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@@ Line 9: / Line 9: @@
 <scene name='NS5B/Native_ns5b/6'>Beta-hairpin in thumb domain</scene> that is proposed to move upon formation of exiting double stranded RNA.
-<applet load='2HAI_DNA5.pdb' size='400' frame='true' align='left' caption='Figure 2. PDB IDs 2HAI (protein) 1RTD (DNA)' />Here is a model of NS5B with B form DNA from HIV Reverse Transcriptase co-crystal model.  DNA was modeled into the NS5B model by aligning of palms domain of NS5B and HIV reverse transcriptase in complex with DNA and an incoming dTTP then removing the HIV RT protein model while leaving the DNA where it fell into the proposed NS5B binding cleft. The catalytic Mg2+ ions are modeled in green, these would be coordinated by the three aspartic acid carboxylates, (D220, D318 and D319). A beta hairpin (residues 440-455) in the thumb domain has been moved to accommodate DNA, the hairpin is modeled into the minor groove, a possible binding site.
+<applet load='2HAI_DNA5.pdb' size='400' frame='true' align='left' caption='Figure 2. PDB IDs 2HAI (protein) 1RTD (DNA)' />Figure 2 is a model of NS5B with B form DNA from HIV Reverse Transcriptase co-crystal model.  DNA was modeled into the NS5B model by aligning of palms domain of NS5B and HIV reverse transcriptase in complex with DNA and an incoming dTTP then removing the HIV RT protein model while leaving the DNA where it fell into the proposed NS5B binding cleft. The catalytic Mg2+ ions are modeled in green, these would be coordinated by the three aspartic acid carboxylates, (D220, D318 and D319). A beta hairpin (residues 440-455) in the thumb domain has been moved to accommodate DNA, the hairpin is modeled into the minor groove, a possible binding site.
 The template strand is seen entering through a gap in the fingers domain. An incoming dTTP that would extend the primer strand lines up with the NS5B active site and duplex DNA exits the enzyme through the large central hole. <scene name='NS5B/Ns5b_with_dna/1'>Active site</scene> <scene name='NS5B/Ns5b_with_dna/2'>Beta-hairpin</scene> P
 <applet load='2HAI_catalytic3.pdb' size='400' frame='true' align='right' caption='Figure 3.' /> <scene name='NS5B/Ns5b_rna_interactions/1'>NS5B RNA interactions</scene>