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[[Image:1yks.gif|left|200px]]<br /><applet load="1yks" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1yks, resolution 1.8&Aring;" />
'''Crystal structure of yellow fever virus NS3 helicase'''<br />


==Overview==
==Crystal structure of yellow fever virus NS3 helicase==
Yellow fever virus (YFV), a member of the Flavivirus genus, has a plus-sense RNA genome encoding a single polyprotein. Viral protein NS3 includes a protease and a helicase that are essential to virus replication and to RNA capping. The 1.8-A crystal structure of the helicase region of the YFV NS3 protein includes residues 187 to 623. Two familiar helicase domains bind nucleotide in a triphosphate pocket without base recognition, providing a site for nonspecific hydrolysis of nucleoside triphosphates and RNA triphosphate. The third, C-terminal domain has a unique structure and is proposed to function in RNA and protein recognition. The organization of the three domains indicates that cleavage of the viral polyprotein NS3-NS4A junction occurs in trans.
<StructureSection load='1yks' size='340' side='right'caption='[[1yks]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1yks]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yellow_fever_virus Yellow fever virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YKS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YKS FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yks FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yks OCA], [https://pdbe.org/1yks PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yks RCSB], [https://www.ebi.ac.uk/pdbsum/1yks PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yks ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/POLG_YEFV1 POLG_YEFV1] Capsid protein C self-assembles to form an icosahedral capsid about 30 nm in diameter. The capsid encapsulates the genomic RNA (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref>  prM acts as a chaperone for envelope protein E during intracellular virion assembly by masking and inactivating envelope protein E fusion peptide. prM is matured in the last step of virion assembly, presumably to avoid catastrophic activation of the viral fusion peptide induced by the acidic pH of the trans-Golgi network. After cleavage by host furin, the pr peptide is released in the extracellular medium and small envelope protein M and envelope protein E homodimers are dissociated (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref>  Envelope protein E binding to host cell surface receptor is followed by virus internalization through clathrin-mediated endocytosis. Envelope protein E is subsequently involved in membrane fusion between virion and host late endosomes. Synthesized as a homodimer with prM which acts as a chaperone for envelope protein E. After cleavage of prM, envelope protein E dissociate from small envelope protein M and homodimerizes (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref>  Non-structural protein 1 is involved in virus replication and regulation of the innate immune response (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref>  Non-structural protein 2A may be involved viral RNA replication and capsid assembly (Potential).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref>  Non-structural protein 2B is a required cofactor for the serine protease function of NS3 (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref>  Serine protease NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS3 serine protease, in association with NS2B, performs its autocleavage and cleaves the polyprotein at dibasic sites in the cytoplasm: C-prM, NS2A-NS2B, NS2B-NS3, NS3-NS4A, NS4A-2K and NS4B-NS5. NS3 RNA helicase binds RNA and unwinds dsRNA in the 3' to 5' direction (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref>  Non-structural protein 4A induces host endoplasmic reticulum membrane rearrangements leading to the formation of virus-induced membranous vesicles hosting the dsRNA and polymerase, functioning as a replication complex. NS4A might also regulate the ATPase activity of the NS3 helicase (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref>  Peptide 2k functions as a signal peptide for NS4B and is required for the interferon antagonism activity of the latter (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref>  Non-structural protein 4B inhibits interferon (IFN)-induced host STAT1 phosphorylation and nuclear translocation, thereby preventing the establishment of cellular antiviral state by blocking the IFN-alpha/beta pathway (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref>  RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome, and performs the capping of genomes in the cytoplasm. NS5 methylates viral RNA cap at guanine N-7 and ribose 2'-O positions. Besides its role in genome replication, also prevents the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) signaling pathway (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yk/1yks_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1yks ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1YKS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Yellow_fever_virus Yellow fever virus]. Active as [http://en.wikipedia.org/wiki/Flavivirin Flavivirin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.91 3.4.21.91] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YKS OCA].
*[[Helicase 3D structures|Helicase 3D structures]]
 
== References ==
==Reference==
<references/>
Structure of the Flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing., Wu J, Bera AK, Kuhn RJ, Smith JL, J Virol. 2005 Aug;79(16):10268-77. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16051820 16051820]
__TOC__
[[Category: Flavivirin]]
</StructureSection>
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Yellow fever virus]]
[[Category: Yellow fever virus]]
[[Category: Bera, A K.]]
[[Category: Bera AK]]
[[Category: Kuhn, R J.]]
[[Category: Kuhn RJ]]
[[Category: Smith, J L.]]
[[Category: Smith JL]]
[[Category: Wu, J.]]
[[Category: Wu J]]
[[Category: atpase]]
[[Category: dead-box]]
[[Category: flavivirus]]
[[Category: helicase]]
[[Category: rtpase]]
[[Category: yellow fever virus]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:06:21 2008''
Retrieved from "https://proteopedia.org/1yks"