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== Dengue Virus Non-Structural Protein NS5 ==
== Dengue Virus Non-Structural Protein NS5 ==
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The dengue virus (DENV) belongs to genus Flavivirus, which also includes the West Nile Virus, Japanese Encephalitis Virus and Yellow Fever Virus. The mosquito-borne DENV causes dengue fever which can then progress to dengue hemorrhagic fever and dengue shock syndrome. Endemic to the tropics and subtropics. It is mainly transmitted by Aedes mosquitoes. Although there are 390 million dengue infections reported annually, no specific antiviral drug or vaccine has been developed yet.
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The dengue virus (DENV) belongs to genus Flavivirus, which also includes the West Nile Virus, Japanese Encephalitis Virus and Yellow Fever Virus. Mosquito-borne DENV causes dengue fever which can then progress to dengue hemorrhagic fever and dengue shock syndrome. Endemic to the tropics and subtropics, it is mainly transmitted by Aedes mosquitoes. Although there are 390 million dengue infections reported annually, no specific antiviral drug or vaccine has been developed yet.
There are four serotypes of the virus (DEN-1 – DEN-4). The viral genome encodes three structural proteins (capsid, membrane and envelope) and seven non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5). By associating with host cofactors and each other, NS proteins form multi-protein replication complexes, which comprise the viral replication machinery. The NS5 primary sequence is generally well conserved across serotypes and also shares some similarity with the NS5 protein of other flaviviruses.
There are four serotypes of the virus (DEN-1 – DEN-4). The viral genome encodes three structural proteins (capsid, membrane and envelope) and seven non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5). By associating with host cofactors and each other, NS proteins form multi-protein replication complexes, which comprise the viral replication machinery. The NS5 primary sequence is generally well conserved across serotypes and also shares some similarity with the NS5 protein of other flaviviruses.
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NS5 is a 104 kDa, 900 amino acid long protein containing a methyltransferase (MTase) domain and a RNA-dependent RNA polymerase (RdRp) domain that are connected by a flexible linker roughly 10 amino acids in length. GREEN LINK The methyltransferase domain runs from residue 6-262, the linker from 263-272, and the RdRp domain from 273-883.
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NS5 is a 104 kDa, 900 amino acid long protein containing a methyltransferase (MTase) domain and a RNA-dependent RNA polymerase (RdRp) domain that are connected by a flexible linker roughly 10 amino acids in length. GREEN LINK The MTase domain comprises residues 6-262, the linker 263-272, and the RdRp domain 273-883.
The RdRp is similar to other polymerases in that it contains finger, thumb and palm subdomains. It also contains two bound zinc atoms located specifically in the finger and thumb subdomains.
The RdRp is similar to other polymerases in that it contains finger, thumb and palm subdomains. It also contains two bound zinc atoms located specifically in the finger and thumb subdomains.
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The linker connects the two domains acting like a swivel and is responsible for their relative orientation to each other. Residues 263-266, located after the MTase C-terminus, are key in this regard. They fold into a short 310 helix resulting in compaction of the polypeptide chain which allows for a large inter-domain interface interaction, giving the protein its globular shape. (GREEN LINK)
The linker connects the two domains acting like a swivel and is responsible for their relative orientation to each other. Residues 263-266, located after the MTase C-terminus, are key in this regard. They fold into a short 310 helix resulting in compaction of the polypeptide chain which allows for a large inter-domain interface interaction, giving the protein its globular shape. (GREEN LINK)
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This flexibility is a key aspect as it has been demonstrated that the linker residues (268-272) N-terminal to the RdRp region enhance stability and polymerase activity and is further evidenced by results showing superior activity in the complete NS5 protein as compared to the RdRp alone, further corroborating that MTase-RdRp interactions are required to maintain RNA synthesis.
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This flexibility is a key feature as it has been demonstrated that the linker residues (268-272) N-terminal to the RdRp region enhance stability and polymerase activity and is further evidenced by results showing superior activity in the complete NS5 protein as compared to the RdRp alone, further corroborating that MTase-RdRp interactions are required to maintain RNA synthesis.
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The inter-domain interface is stabilized by several polar contacts between residues projecting from the MTase and RdRp domains of NS5. These interactions are as follows
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The inter-domain is made up of two clusters which involve residues from linker region, the RdRp finger subdomain, and the MTase domain.
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The majority of the stabilizing interactions within the inter-domain interface are polar in nature, resulting from those between charged side-chains as well as hydrogen-bonding mediated by trapped water molecules. The inter-domain is made up of two clusters which involve residues from linker region, the RdRp finger subdomain, and the MTase domain.
1st cluster:
1st cluster:
Interaction of linker residues with both RdRp and MTase domains. Linker residue E267's side chain hydrogen bonds with with residues Y119 and R262 of the MTase domain with E269 forming a salt-bridge with RdRp domain's R361. Polar interactions between residues from the MTase domain (K95 & K96) and the RdRp domain (E296-K300) also play an important role in the cluster.
Interaction of linker residues with both RdRp and MTase domains. Linker residue E267's side chain hydrogen bonds with with residues Y119 and R262 of the MTase domain with E269 forming a salt-bridge with RdRp domain's R361. Polar interactions between residues from the MTase domain (K95 & K96) and the RdRp domain (E296-K300) also play an important role in the cluster.
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2nd cluster:
2nd cluster:
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Based at α5 helix residues (F348-K357)in the RdRp domain of which guanidinium of R352 interacts electrostatically with a number of residues in the MTase domain (E67, E252, Q63).
Based at α5 helix residues (F348-K357)in the RdRp domain of which 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.
A salt-bridge is also formed between K357 and D256.
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Trapped water molecules in the interface regulate hydrogen bonding interactions between residues from both domains
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== Function ==
== Function ==

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Aedes Aegypti mosquito
Aedes Aegypti mosquito


Dengue Virus Non-Structural Protein NS5

The dengue virus (DENV) belongs to genus Flavivirus, which also includes the West Nile Virus, Japanese Encephalitis Virus and Yellow Fever Virus. Mosquito-borne DENV causes dengue fever which can then progress to dengue hemorrhagic fever and dengue shock syndrome. Endemic to the tropics and subtropics, it is mainly transmitted by Aedes mosquitoes. Although there are 390 million dengue infections reported annually, no specific antiviral drug or vaccine has been developed yet.

There are four serotypes of the virus (DEN-1 – DEN-4). The viral genome encodes three structural proteins (capsid, membrane and envelope) and seven non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5). By associating with host cofactors and each other, NS proteins form multi-protein replication complexes, which comprise the viral replication machinery. The NS5 primary sequence is generally well conserved across serotypes and also shares some similarity with the NS5 protein of other flaviviruses.

[1]


[2]

Structure

DENV NS5 (4V0Q)

Cartoon view of NS5

Drag the structure with the mouse to rotate

References

  1. ↑ Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, Drake JM, Brownstein JS, Hoen AG, Sankoh O, Myers MF, George DB, Jaenisch T, Wint GR, Simmons CP, Scott TW, Farrar JJ, Hay SI. The global distribution and burden of dengue. Nature. 2013 Apr 25;496(7446):504-7. doi: 10.1038/nature12060. Epub 2013 Apr 7. PMID:23563266 doi:http://dx.doi.org/10.1038/nature12060
  2. ↑ Potisopon S, Priet S, Collet A, Decroly E, Canard B, Selisko B. The methyltransferase domain of dengue virus protein NS5 ensures efficient RNA synthesis initiation and elongation by the polymerase domain. Nucleic Acids Res. 2014 Oct;42(18):11642-56. doi: 10.1093/nar/gku666. Epub 2014, Sep 10. PMID:25209234 doi:http://dx.doi.org/10.1093/nar/gku666
  3. ↑ Zhao Y, Soh TS, Zheng J, Chan KW, Phoo WW, Lee CC, Tay MY, Swaminathan K, Cornvik TC, Lim SP, Shi PY, Lescar J, Vasudevan SG, Luo D. A Crystal Structure of the Dengue Virus NS5 Protein Reveals a Novel Inter-domain Interface Essential for Protein Flexibility and Virus Replication. PLoS Pathog. 2015 Mar 16;11(3):e1004682. doi: 10.1371/journal.ppat.1004682., eCollection 2015 Mar. PMID:25775415 doi:http://dx.doi.org/10.1371/journal.ppat.1004682
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