Sandbox Reserved 1688: Difference between revisions

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'''NS5B''' is the '''RNA dependent RNA polymerase''' of Hepatitis C virus. NS5B, like other RNA dependent RNA polymerases, is error prone. This viral RNA replicase is of 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. IN NS5B two divalent cations coordinated by carboxyl groups (as seen in DNA polymerases) catalyze the polymerization of monomers of RNA triphosphates to extend a primer strand, that may have initiated ''de novo''. In the case of NS5B the residues that coordinate divalent cations <scene name='89/891378/Palmcordmagnesium/3'>residues that coordinate divalent cations </scene>(Mg2+ or Mn2+ ''in vitro'') are the three seen here (PDB entry [[2hai]]).

Though Hepatitis C virus is of the Flaviviridae family the structure of NS5B is similar to the polymerase of bacteriophage Φ 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, fingers in blue, palm in magenta, thumb in green and a c-terminal domain in yellow. Specific to Hepatitis C virus family, the NS5B protein has a 21-24 residue hydrophobic membrane anchor at its C-termini that allows involvement with the replication complex that is located in membrane bound vesicles derived from the endoplasmic reticulum. The fingers, palm, and thumb region of the NS5B contain 531 residues and are composed of 21 alpha helices and 18 beta barrels. The fingers region of NS5B can be divided into two distinct sections: the palm-proximal region and the distal region. The palm-proximal region is folded as a bundle of alpha helices and the distal region is composed of a singular beta barrel. These regions are termed the fingertips. The fingers domain interacts with the major groove of the template RNA and aids in recognition and binding. The main residues responsible for binding are <scene name='89/891378/Residues_91-94/1'>91-94~~</scene>~~ and ~~<scene name='89/891378/Residues_168-183/1'>~~168-183</scene>. The fingers domain of NS5B are composed of a set of 4 beta strands that can establish contact with the thumb region closing the active site. The thumb region of HCV is structurally larger in comparison to other RdRps. It is composed mainly of alpha helices, 7 of them, and two beta hairpins. It contains amino acids 370-531 termed the <scene name='89/891378/Thumbregion/1'>Thumb Region</scene>. One is a that is proposed to move upon formation of exiting double-stranded RNA. The core of the thumb is composed of two repeating helix motifs. The thumb region of NS5B also contains a “priming loop” that extends from the thumb and provides stability during initiation. 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.

Though Hepatitis C virus is of the Flaviviridae family the structure of NS5B is similar to the polymerase of bacteriophage Φ 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, fingers in blue, palm in magenta, thumb in green and a c-terminal domain in yellow. Specific to Hepatitis C virus family, the NS5B protein has a 21-24 residue hydrophobic membrane anchor at its C-termini that allows involvement with the replication complex that is located in membrane bound vesicles derived from the endoplasmic reticulum. The fingers, palm, and thumb region of the NS5B contain 531 residues and are composed of 21 alpha helices and 18 beta barrels. The fingers region of NS5B can be divided into two distinct sections: the palm-proximal region and the distal region. The palm-proximal region is folded as a bundle of alpha helices and the distal region is composed of a singular beta barrel. These regions are termed the fingertips. The fingers domain interacts with the major groove of the template RNA and aids in recognition and binding. The main residues responsible for binding are <scene name='89/891378/Residues_91-94_and_168-183/1'>91-94 and 168-183</scene>. The fingers domain of NS5B are composed of a set of 4 beta strands that can establish contact with the thumb region closing the active site. The thumb region of HCV is structurally larger in comparison to other RdRps. It is composed mainly of alpha helices, 7 of them, and two beta hairpins. It contains amino acids 370-531 termed the <scene name='89/891378/Thumbregion/1'>Thumb Region</scene>. One is a that is proposed to move upon formation of exiting double-stranded RNA. The core of the thumb is composed of two repeating helix motifs. The thumb region of NS5B also contains a “priming loop” that extends from the thumb and provides stability during initiation. 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.

Sandbox Reserved 1688: Difference between revisions

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Revision as of 03:49, 12 October 2021 view source Kody Witham (talk \| contribs) 42 edits No edit summary ← Older edit		Revision as of 03:56, 12 October 2021 view source Kody Witham (talk \| contribs) 42 edits No edit summary Newer edit →
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	'''NS5B''' is the '''RNA dependent RNA polymerase''' of Hepatitis C virus. NS5B, like other RNA dependent RNA polymerases, is error prone. This viral RNA replicase is of 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. IN NS5B two divalent cations coordinated by carboxyl groups (as seen in DNA polymerases) catalyze the polymerization of monomers of RNA triphosphates to extend a primer strand, that may have initiated ''de novo''. In the case of NS5B the residues that coordinate divalent cations <scene name='89/891378/Palmcordmagnesium/3'>residues that coordinate divalent cations </scene>(Mg2+ or Mn2+ ''in vitro'') are the three seen here (PDB entry [[2hai]]).		'''NS5B''' is the '''RNA dependent RNA polymerase''' of Hepatitis C virus. NS5B, like other RNA dependent RNA polymerases, is error prone. This viral RNA replicase is of 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. IN NS5B two divalent cations coordinated by carboxyl groups (as seen in DNA polymerases) catalyze the polymerization of monomers of RNA triphosphates to extend a primer strand, that may have initiated ''de novo''. In the case of NS5B the residues that coordinate divalent cations <scene name='89/891378/Palmcordmagnesium/3'>residues that coordinate divalent cations </scene>(Mg2+ or Mn2+ ''in vitro'') are the three seen here (PDB entry [[2hai]]).

	Though Hepatitis C virus is of the Flaviviridae family the structure of NS5B is similar to the polymerase of bacteriophage Φ 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, fingers in blue, palm in magenta, thumb in green and a c-terminal domain in yellow. Specific to Hepatitis C virus family, the NS5B protein has a 21-24 residue hydrophobic membrane anchor at its C-termini that allows involvement with the replication complex that is located in membrane bound vesicles derived from the endoplasmic reticulum. The fingers, palm, and thumb region of the NS5B contain 531 residues and are composed of 21 alpha helices and 18 beta barrels. The fingers region of NS5B can be divided into two distinct sections: the palm-proximal region and the distal region. The palm-proximal region is folded as a bundle of alpha helices and the distal region is composed of a singular beta barrel. These regions are termed the fingertips. The fingers domain interacts with the major groove of the template RNA and aids in recognition and binding. The main residues responsible for binding are <scene name='89/891378/Residues_91-94/1'>91-94~~</scene>~~ and ~~<scene name='89/891378/Residues_168-183/1'>~~168-183</scene>. The fingers domain of NS5B are composed of a set of 4 beta strands that can establish contact with the thumb region closing the active site. The thumb region of HCV is structurally larger in comparison to other RdRps. It is composed mainly of alpha helices, 7 of them, and two beta hairpins. It contains amino acids 370-531 termed the <scene name='89/891378/Thumbregion/1'>Thumb Region</scene>. One is a that is proposed to move upon formation of exiting double-stranded RNA. The core of the thumb is composed of two repeating helix motifs. The thumb region of NS5B also contains a “priming loop” that extends from the thumb and provides stability during initiation. 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.		Though Hepatitis C virus is of the Flaviviridae family the structure of NS5B is similar to the polymerase of bacteriophage Φ 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, fingers in blue, palm in magenta, thumb in green and a c-terminal domain in yellow. Specific to Hepatitis C virus family, the NS5B protein has a 21-24 residue hydrophobic membrane anchor at its C-termini that allows involvement with the replication complex that is located in membrane bound vesicles derived from the endoplasmic reticulum. The fingers, palm, and thumb region of the NS5B contain 531 residues and are composed of 21 alpha helices and 18 beta barrels. The fingers region of NS5B can be divided into two distinct sections: the palm-proximal region and the distal region. The palm-proximal region is folded as a bundle of alpha helices and the distal region is composed of a singular beta barrel. These regions are termed the fingertips. The fingers domain interacts with the major groove of the template RNA and aids in recognition and binding. The main residues responsible for binding are <scene name='89/891378/Residues_91-94_and_168-183/1'>91-94 and 168-183</scene>. The fingers domain of NS5B are composed of a set of 4 beta strands that can establish contact with the thumb region closing the active site. The thumb region of HCV is structurally larger in comparison to other RdRps. It is composed mainly of alpha helices, 7 of them, and two beta hairpins. It contains amino acids 370-531 termed the <scene name='89/891378/Thumbregion/1'>Thumb Region</scene>. One is a that is proposed to move upon formation of exiting double-stranded RNA. The core of the thumb is composed of two repeating helix motifs. The thumb region of NS5B also contains a “priming loop” that extends from the thumb and provides stability during initiation. 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.