Sandbox Reserved 1088: Difference between revisions

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== Methyltransferase domain ==

The <scene name='70/700001/4v0q_mtase/3'>MTase domain</scene> is involved in 5’ capping of the newly synthesized RNA - it catalyzes RNA cap methylation at both the N7 position on the guanosine and the 2’O on the subsequent nucleotide of the newly synthesized (+) RNA strand<ref name= "Wu"/><ref name= "Zhao">PMID:25775415</ref>. The MTase domain contains five parallel beta sheets and within NS5, lies above the finger subdomain of RdRp in such an orientation that its catalytic core (K61-D146-K180-E216) and ~~SAH~~ binding pockets face away from the inter-domain interface <ref name= "Zhao"/>.

The <scene name='70/700001/4v0q_mtase/3'>MTase domain</scene> is involved in 5’ capping of the newly synthesized RNA - it catalyzes RNA cap methylation at both the N7 position on the guanosine and the 2’O on the subsequent nucleotide of the newly synthesized (+) RNA strand<ref name= "Wu"/><ref name= "Zhao">PMID:25775415</ref>. The MTase domain contains five parallel beta sheets and within NS5, lies above the finger subdomain of RdRp in such an orientation that its catalytic core (K61-D146-K180-E216) and SAM binding pockets face away from the inter-domain interface <ref name= "Zhao"/>.

== RNA-dependent RNA polymerase domain ==

The <scene name='70/700001/4v0q_rdrp/2'>RdRp domain</scene> is responsible for the replication and transcription of the viral genome and new viral RNA is synthesized without the need for a primer (''de novo'' RNA synthesis). Like other polymerases, the RdRp is similar in that it contains finger, thumb, and palm subdomains as well as making use of a common catalytic mechanism for nucleotide incorporation involving two metal ions (zinc in NS5) located in the finger and thumb subdomains<ref name= "Yap"/>. Together, the thumb and finger subdomains form a <scene name='70/700001/4v0q_rdrpp/1'>tunnel</scene> through which the RNA template and nucleotides enter en route to the catalytic core within the palm subdomain. Inside the tunnel, a priming loop protrudes from a thumb subdomain towards the active site and is critical in ''de novo'' initiation<ref name= "Yap"/><ref name= "Wu"/>. The RdRp is a feature unique to viruses and may be considered as a target for antiviral therapy.

The <scene name='70/700001/4v0q_rdrp/2'>RdRp domain</scene> is responsible for the replication and transcription of the viral genome and new viral RNA is synthesized without the need for a primer (''de novo'' RNA synthesis). Like other polymerases, the RdRp is similar in that it contains finger, thumb, and palm subdomains orientated in the canonical right-hand conformation as well as making use of a common catalytic mechanism for nucleotide incorporation involving two metal ions (zinc in NS5) located in the finger and thumb subdomains<ref name= "Yap"/>. The entire RdRp domain is comprised of a total of 27 α-helices and seven β-sheets

Together, the thumb and finger subdomains form a <scene name='70/700001/4v0q_rdrpp/1'>tunnel</scene> through which the RNA template and nucleotides enter en route to the catalytic core within the palm subdomain. Inside the tunnel, a priming loop protrudes from a thumb subdomain towards the active site where it controls access to and exit into the catalytic core and is thus critical in ''de novo'' initiation<ref name= "Yap"/><ref name= "Wu"/>. The RdRp is a feature unique to viruses and may be considered as a target for antiviral therapy.

<br>

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In the first cluster, interaction of linker residues with both RdRp and MTase domains is observed. Specifically, linker residue E267's side chain hydrogen bonds with residues Y119 and R262 of the MTase domain while E269 forms a salt-bridge with R361 of the RdRp domain. Polar interactions between residues from the MTase domain (K95 & K96) and the RdRp domain (E296-K300) also play an important role in the cluster.

The second cluster is based at <scene name='70/700001/4v0q_rdrp/3'>α5 ~~helix~~</scene> residues (F348-K357) in the RdRp domain where guanidinium of R352 interacts electrostatically with a number of residues in the MTase domain (E67, E252, Q63). A salt-bridge is also formed between K357 and D256. Though hydrophobic interactions are not as numerous as hydrophilic interactions, they do exist as stacking interactions, namely between W64, R68, F348, and P582<ref name= "Zhao"/>.

The second cluster is based at <scene name='70/700001/4v0q_rdrp/3'>helix α5</scene> residues (F348-K357) in the RdRp domain where guanidinium of R352 interacts electrostatically with a number of residues in the MTase domain (E67, E252, Q63). A salt-bridge is also formed between K357 and D256. Though hydrophobic interactions are not as numerous as hydrophilic interactions, they do exist as stacking interactions, namely between W64, R68, F348, and P582<ref name= "Zhao"/>.

Through mutation studies in '''DENV-4''', residues K95 and R353 have been specifically implicated in critical but non-enzymatic roles in virus RNA replication and infectivity while Y119 has been shown to be necessary for MTase activity and therefore a requirement for viral replication. Because of a majority of polar interactions as well as a small inter-domain buried surface area (1502 Å), it has been suggested that the two enzymatic domains may be able to associate and dissociate from each other with a relatively small energy penalty. Additionally, this dynamic interaction may also lend itself to facilitating the recruitment of other viral and host proteins as part of the replication complex<ref name= "Zhao"/>.

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@@ Line 26: / Line 26: @@
 == Methyltransferase domain ==
-The <scene name='70/700001/4v0q_mtase/3'>MTase domain</scene> is involved in 5’ capping of the newly synthesized RNA - it catalyzes RNA cap methylation at both the N7 position on the guanosine and the 2’O on the subsequent nucleotide of the newly synthesized (+) RNA strand<ref name= "Wu"/><ref name= "Zhao">PMID:25775415</ref>. The MTase domain contains five parallel beta sheets and within NS5, lies above the finger subdomain of RdRp in such an orientation that its catalytic core (K61-D146-K180-E216) and SAH binding pockets face away from the inter-domain interface <ref name= "Zhao"/>.
+The <scene name='70/700001/4v0q_mtase/3'>MTase domain</scene> is involved in 5’ capping of the newly synthesized RNA - it catalyzes RNA cap methylation at both the N7 position on the guanosine and the 2’O on the subsequent nucleotide of the newly synthesized (+) RNA strand<ref name= "Wu"/><ref name= "Zhao">PMID:25775415</ref>. The MTase domain contains five parallel beta sheets and within NS5, lies above the finger subdomain of RdRp in such an orientation that its catalytic core (K61-D146-K180-E216) and SAM binding pockets face away from the inter-domain interface <ref name= "Zhao"/>.
 == RNA-dependent RNA polymerase domain ==
-The <scene name='70/700001/4v0q_rdrp/2'>RdRp domain</scene> is responsible for the replication and transcription of the viral genome and new viral RNA is synthesized without the need for a primer (''de novo'' RNA synthesis). Like other polymerases, the RdRp is similar in that it contains finger, thumb, and palm subdomains as well as making use of a common catalytic mechanism for nucleotide incorporation involving two metal ions (zinc in NS5) located in the finger and thumb subdomains<ref name= "Yap"/>. Together, the thumb and finger subdomains form a <scene name='70/700001/4v0q_rdrpp/1'>tunnel</scene> through which the RNA template and nucleotides enter en route to the catalytic core within the palm subdomain. Inside the tunnel, a priming loop protrudes from a thumb subdomain towards the active site and is critical in ''de novo'' initiation<ref name= "Yap"/><ref name= "Wu"/>. The RdRp is a feature unique to viruses and may be considered as a target for antiviral therapy.
+The <scene name='70/700001/4v0q_rdrp/2'>RdRp domain</scene> is responsible for the replication and transcription of the viral genome and new viral RNA is synthesized without the need for a primer (''de novo'' RNA synthesis). Like other polymerases, the RdRp is similar in that it contains finger, thumb, and palm subdomains orientated in the canonical right-hand conformation as well as making use of a common catalytic mechanism for nucleotide incorporation involving two metal ions (zinc in NS5) located in the finger and thumb subdomains<ref name= "Yap"/>. The entire RdRp domain is comprised of a total of 27 α-helices and seven β-sheets
+Together, the thumb and finger subdomains form a <scene name='70/700001/4v0q_rdrpp/1'>tunnel</scene> through which the RNA template and nucleotides enter en route to the catalytic core within the palm subdomain. Inside the tunnel, a priming loop protrudes from a thumb subdomain towards the active site where it controls access to and exit into the catalytic core and is thus critical in ''de novo'' initiation<ref name= "Yap"/><ref name= "Wu"/>. The RdRp is a feature unique to viruses and may be considered as a target for antiviral therapy.
 <br>
@@ Line 52: / Line 54: @@
 In the first cluster, interaction of linker residues with both RdRp and MTase domains is observed. Specifically, linker residue E267's side chain hydrogen bonds with residues Y119 and R262 of the MTase domain while E269 forms a salt-bridge with R361 of the RdRp domain. Polar interactions between residues from the MTase domain (K95 & K96) and the RdRp domain (E296-K300) also play an important role in the cluster.
-The second cluster is based at <scene name='70/700001/4v0q_rdrp/3'>α5 helix</scene> residues (F348-K357) in the RdRp domain where guanidinium of R352 interacts electrostatically with a number of residues in the MTase domain (E67, E252, Q63). A salt-bridge is also formed between K357 and D256. Though hydrophobic interactions are not as numerous as hydrophilic interactions, they do exist as stacking interactions, namely between W64, R68, F348, and P582<ref name= "Zhao"/>.
+The second cluster is based at <scene name='70/700001/4v0q_rdrp/3'>helix α5</scene> residues (F348-K357) in the RdRp domain where guanidinium of R352 interacts electrostatically with a number of residues in the MTase domain (E67, E252, Q63). A salt-bridge is also formed between K357 and D256. Though hydrophobic interactions are not as numerous as hydrophilic interactions, they do exist as stacking interactions, namely between W64, R68, F348, and P582<ref name= "Zhao"/>.
 Through mutation studies in '''DENV-4''', residues K95 and R353 have been specifically implicated in critical but non-enzymatic roles in virus RNA replication and infectivity while Y119 has been shown to be necessary for MTase activity and therefore a requirement for viral replication. Because of a majority of polar interactions as well as a small inter-domain buried surface area (1502 Å), it has been suggested that the two enzymatic domains may be able to associate and dissociate from each other with a relatively small energy penalty. Additionally, this dynamic interaction may also lend itself to facilitating the recruitment of other viral and host proteins as part of the replication complex<ref name= "Zhao"/>.