NS5B: Difference between revisions

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<applet load='2HAI_catalytic3.pdb' size='400' frame='true' align='right' caption='PDB ID 2HAI' />NS5B is the RNA dependent RNA polymerase of Hepatitis C virus. NS5B, like other RNA dependent RNA polymerases, is error prone, it is approximately a million times lower fidelity than a replicative prokayrotic or eukaryotic DNA polymerase. This is due in part to the fact that NS5B contains no exonuclease or proofreading domain. The proposed mechanism for NS5B polymerization of monomers of RNA triphosphates to extend a primer strand, that may have initiated de novo, is via two divalent cations coordinated by carboxyl groups as seen in DNA polymerases. In the case of NS5B the residues that coordinate divalent cations (Mg2+ or Mn2+ in vitro) are the

<applet load='2HAI_catalytic3.pdb' size='400' frame='true' align='right' caption='PDB ID 2HAI' />NS5B is the RNA dependent RNA polymerase of Hepatitis C virus. NS5B, like other RNA dependent RNA polymerases, is error prone, it is approximately a million times lower fidelity than a replicative prokayrotic or eukaryotic DNA polymerase. This is due in part to the fact that NS5B contains no exonuclease or proofreading domain. The proposed mechanism for NS5B polymerization of monomers of RNA triphosphates to extend a primer strand, that may have initiated de novo, is via two divalent cations coordinated by carboxyl groups as seen in DNA polymerases. In the case of NS5B the residues that coordinate divalent cations (Mg2+ or Mn2+ in vitro) are the three

<scene name='NS5B/Native_ns5b/4'>~~three~~ active site aspartates</scene> seen here.

<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

<scene name='NS5B/Native_ns5b/3'>~~Domains~~</scene>

<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/6'>Beta-hairpin in thumb domain</scene>

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-<applet load='2HAI_catalytic3.pdb' size='400' frame='true' align='right' caption='PDB ID 2HAI' />NS5B is the RNA dependent RNA polymerase of Hepatitis C virus. NS5B, like other RNA dependent RNA polymerases, is error prone, it is approximately a million times lower fidelity than a replicative prokayrotic or eukaryotic DNA polymerase. This is due in part to the fact that NS5B contains no exonuclease or proofreading domain. The proposed mechanism for NS5B polymerization of monomers of RNA triphosphates to extend a primer strand, that may have initiated de novo, is via two divalent cations coordinated by carboxyl groups as seen in DNA polymerases. In the case of NS5B the residues that coordinate divalent cations (Mg2+ or Mn2+ in vitro) are the
+<applet load='2HAI_catalytic3.pdb' size='400' frame='true' align='right' caption='PDB ID 2HAI' />NS5B is the RNA dependent RNA polymerase of Hepatitis C virus. NS5B, like other RNA dependent RNA polymerases, is error prone, it is approximately a million times lower fidelity than a replicative prokayrotic or eukaryotic DNA polymerase. This is due in part to the fact that NS5B contains no exonuclease or proofreading domain. The proposed mechanism for NS5B polymerization of monomers of RNA triphosphates to extend a primer strand, that may have initiated de novo, is via two divalent cations coordinated by carboxyl groups as seen in DNA polymerases. In the case of NS5B the residues that coordinate divalent cations (Mg2+ or Mn2+ in vitro) are the three
-<scene name='NS5B/Native_ns5b/4'>three active site aspartates</scene> seen here.
+<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
-<scene name='NS5B/Native_ns5b/3'>Domains</scene>
+<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/6'>Beta-hairpin in thumb domain</scene>