NS5B: Difference between revisions

Line 5:

<scene name='NS5B/Native_ns5b/4'>active site aspartates (220, 318 and 319)</scene> seen here.

Though Hepatitis C virus is of the Flaviviridae family the structure of NS5B is similar to the polymerase of bacteriophage ø 6. Like many template-dependent nucleotide polymerases, NS5B can be visualized similar to a right hand. NS5B contains several

Though Hepatitis C virus is of the Flaviviridae family the structure of NS5B is similar to the polymerase of bacteriophage ø 6. The similarity to the bacteriophage polymerase is due to NS5B containing a fully encircled active site. Like many template-dependent nucleotide polymerases, NS5B can be visualized similar to a right hand. NS5B contains several

<scene name='NS5B/Native_ns5b/3'>domains</scene>, fingers in blue, palm in magenta, thumb in green and a c-terminal domain in yellow. The palm domain contains the active site aspartates.

<scene name='NS5B/Native_ns5b/3'>domains</scene>, fingers in blue, palm in magenta, thumb in green and a c-terminal domain in yellow. The palm domain contains the active site aspartates and there are several contacts between the fingers and thumbs domain that give the active site an encircled structure. There is a

<scene name='NS5B/Native_ns5b/6'>Beta-hairpin in thumb domain</scene>

<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='PDB IDs 2HAI (protein) 1RTD (DNA)' />NS5B with B form DNA from HIV Reverse Transcriptase co-crystal model. DNA was modeled in by alignment of palms domain. 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. Catalytic Mg2+ ions are modeled in green, these would be coordinated by the three aspartic acid carboxylates, (D220, D318 and D319).

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@@ Line 5: / Line 5: @@
 <scene name='NS5B/Native_ns5b/4'>active site aspartates (220, 318 and 319)</scene> seen here.
-Though Hepatitis C virus is of the Flaviviridae family the structure of NS5B is similar to the polymerase of bacteriophage ø 6. Like many template-dependent nucleotide polymerases, NS5B can be visualized similar to a right hand. NS5B contains several
+Though Hepatitis C virus is of the Flaviviridae family the structure of NS5B is similar to the polymerase of bacteriophage ø 6. The similarity to the bacteriophage polymerase is due to NS5B containing a fully encircled active site. Like many template-dependent nucleotide polymerases, NS5B can be visualized similar to a right hand. NS5B contains several
-<scene name='NS5B/Native_ns5b/3'>domains</scene>, fingers in blue, palm in magenta, thumb in green and a c-terminal domain in yellow. The palm domain contains the active site aspartates.
+<scene name='NS5B/Native_ns5b/3'>domains</scene>, fingers in blue, palm in magenta, thumb in green and a c-terminal domain in yellow. The palm domain contains the active site aspartates and there are several contacts between the fingers and thumbs domain that give the active site an encircled structure. There is a
-<scene name='NS5B/Native_ns5b/6'>Beta-hairpin in thumb domain</scene>
+<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='PDB IDs 2HAI (protein) 1RTD (DNA)' />NS5B with B form DNA from HIV Reverse Transcriptase co-crystal model.  DNA was modeled in by alignment of palms domain. 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. Catalytic Mg2+ ions are modeled in green, these would be coordinated by the three aspartic acid carboxylates, (D220, D318 and D319).