5dg6: Difference between revisions

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<StructureSection load='5dg6' size='340' side='right'caption='[[5dg6]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
<StructureSection load='5dg6' size='340' side='right'caption='[[5dg6]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5dg6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Hu/nv/nv/1968/us Hu/nv/nv/1968/us]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DG6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5DG6 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5dg6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Norovirus_Hu/1968/US Norovirus Hu/1968/US]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DG6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DG6 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=V66:TERT-BUTYL+[(4S,7S,10S)-7-(CYCLOHEXYLMETHYL)-10-(HYDROXYMETHYL)-5,8,13-TRIOXO-23-OXA-6,9,14,21,22-PENTAAZABICYCLO[18.2.1]TRICOSA-1(22),20-DIEN-4-YL]CARBAMATE'>V66</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=V66:TERT-BUTYL+[(4S,7S,10S)-7-(CYCLOHEXYLMETHYL)-10-(HYDROXYMETHYL)-5,8,13-TRIOXO-23-OXA-6,9,14,21,22-PENTAAZABICYCLO[18.2.1]TRICOSA-1(22),20-DIEN-4-YL]CARBAMATE'>V66</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5dgj|5dgj]]</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=5dg6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dg6 OCA], [https://pdbe.org/5dg6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5dg6 RCSB], [https://www.ebi.ac.uk/pdbsum/5dg6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5dg6 ProSAT]</span></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ORF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=524364 Hu/NV/NV/1968/US])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Calicivirin Calicivirin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.66 3.4.22.66] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5dg6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5dg6 OCA], [http://pdbe.org/5dg6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5dg6 RCSB], [http://www.ebi.ac.uk/pdbsum/5dg6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5dg6 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/POLG_NVN68 POLG_NVN68]] Protein p48 may play a role in viral replication by interacting with host VAPA, a vesicle-associated membrane protein that plays a role in SNARE-mediated vesicle fusion. This interaction may target replication complex to intracellular membranes.<ref>PMID:569187</ref> <ref>PMID:11160659</ref>  NTPase presumably plays a role in replication. Despite having similarities with helicases, does not seem to display any helicase activity.<ref>PMID:569187</ref> <ref>PMID:11160659</ref>  Protein P22 may play a role in targeting replication complex to intracellular membranes.<ref>PMID:569187</ref> <ref>PMID:11160659</ref>  Viral genome-linked protein is covalently linked to the 5'-end of the positive-strand, negative-strand genomic RNAs and subgenomic RNA. Acts as a genome-linked replication primer. May recruit ribosome to viral RNA thereby promoting viral proteins translation.<ref>PMID:569187</ref> <ref>PMID:11160659</ref>  3C-like protease processes the polyprotein: 3CLpro-RdRp is first released by autocleavage, then all other proteins are cleaved. May cleave host polyadenylate-binding protein thereby inhibiting cellular translation (By similarity).<ref>PMID:569187</ref> <ref>PMID:11160659</ref>  RNA-directed RNA polymerase replicates genomic and antigenomic RNA by recognizing replications specific signals. Transcribes also a subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This sgRNA encodes for structural proteins. Catalyzes the covalent attachment VPg with viral RNAs (By similarity).<ref>PMID:569187</ref> <ref>PMID:11160659</ref>
[https://www.uniprot.org/uniprot/POLG_NVN68 POLG_NVN68] Protein p48 may play a role in viral replication by interacting with host VAPA, a vesicle-associated membrane protein that plays a role in SNARE-mediated vesicle fusion. This interaction may target replication complex to intracellular membranes.<ref>PMID:569187</ref> <ref>PMID:11160659</ref>  NTPase presumably plays a role in replication. Despite having similarities with helicases, does not seem to display any helicase activity.<ref>PMID:569187</ref> <ref>PMID:11160659</ref>  Protein P22 may play a role in targeting replication complex to intracellular membranes.<ref>PMID:569187</ref> <ref>PMID:11160659</ref>  Viral genome-linked protein is covalently linked to the 5'-end of the positive-strand, negative-strand genomic RNAs and subgenomic RNA. Acts as a genome-linked replication primer. May recruit ribosome to viral RNA thereby promoting viral proteins translation.<ref>PMID:569187</ref> <ref>PMID:11160659</ref>  3C-like protease processes the polyprotein: 3CLpro-RdRp is first released by autocleavage, then all other proteins are cleaved. May cleave host polyadenylate-binding protein thereby inhibiting cellular translation (By similarity).<ref>PMID:569187</ref> <ref>PMID:11160659</ref>  RNA-directed RNA polymerase replicates genomic and antigenomic RNA by recognizing replications specific signals. Transcribes also a subgenomic mRNA by initiating RNA synthesis internally on antigenomic RNA. This sgRNA encodes for structural proteins. Catalyzes the covalent attachment VPg with viral RNAs (By similarity).<ref>PMID:569187</ref> <ref>PMID:11160659</ref>  
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== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
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==See Also==
==See Also==
*[[SARS Coronavirus Main Proteinase|SARS Coronavirus Main Proteinase]]
*[[Virus protease 3D structures|Virus protease 3D structures]]
*[[Virus proteases 3D strutures|Virus proteases 3D strutures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Calicivirin]]
[[Category: Hu/nv/nv/1968/us]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Alliston, K R]]
[[Category: Norovirus Hu/1968/US]]
[[Category: Battaile, K P]]
[[Category: Alliston KR]]
[[Category: Chang, K O]]
[[Category: Battaile KP]]
[[Category: Damalanka, V C]]
[[Category: Chang K-O]]
[[Category: Groutas, W C]]
[[Category: Damalanka VC]]
[[Category: Kankanamalage, A C.G]]
[[Category: Groutas WC]]
[[Category: Kim, Y]]
[[Category: Kankanamalage ACG]]
[[Category: Lovell, S]]
[[Category: Kim Y]]
[[Category: Lushington, G H]]
[[Category: Lovell S]]
[[Category: Mehzabeen, N]]
[[Category: Lushington GH]]
[[Category: Weerawarna, P M]]
[[Category: Mehzabeen N]]
[[Category: Antiviral inhibitor]]
[[Category: Weerawarna PM]]
[[Category: Cell permeable]]
[[Category: Hydrolase-hydrolase inhibitor complex]]
[[Category: Norovirus]]
[[Category: Norwalk virus]]
[[Category: Oxadiazole inhibitor]]
[[Category: Protease]]
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