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[[Image:3bso.jpg|left|200px]]
==Norwalk Virus polymerase bound to cytidine 5'-triphosphate and primer-template RNA==
 
<StructureSection load='3bso' size='340' side='right' caption='[[3bso]], [[Resolution|resolution]] 1.74&Aring;' scene=''>
{{Structure
== Structural highlights ==
|PDB= 3bso |SIZE=350|CAPTION= <scene name='initialview01'>3bso</scene>, resolution 1.74&Aring;
<table><tr><td colspan='2'>[[3bso]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Norwalk_calicivirus Norwalk calicivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BSO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BSO FirstGlance]. <br>
|SITE= <scene name='pdbsite=AC1:Mn+Binding+Site+For+Residue+A+511'>AC1</scene>, <scene name='pdbsite=AC2:Mn+Binding+Site+For+Residue+A+512'>AC2</scene>, <scene name='pdbsite=AC3:Mn+Binding+Site+For+Residue+A+513'>AC3</scene>, <scene name='pdbsite=AC4:Ctp+Binding+Site+For+Residue+A+514'>AC4</scene>, <scene name='pdbsite=AC5:Gol+Binding+Site+For+Residue+A+515'>AC5</scene>, <scene name='pdbsite=AC6:Gol+Binding+Site+For+Residue+P+9'>AC6</scene>, <scene name='pdbsite=AC7:Gol+Binding+Site+For+Residue+A+516'>AC7</scene> and <scene name='pdbsite=AC8:Gol+Binding+Site+For+Residue+T+10'>AC8</scene>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CTP:CYTIDINE-5-TRIPHOSPHATE'>CTP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
|LIGAND= <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=CTP:CYTIDINE-5&#39;-TRIPHOSPHATE'>CTP</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1sh0|1sh0]], [[3bsn|3bsn]]</td></tr>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] </span>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">polymerase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11983 Norwalk calicivirus])</td></tr>
|GENE= polymerase ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11983 Norwalk virus])
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/RNA-directed_RNA_polymerase RNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.48 2.7.7.48] </span></td></tr>
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd01699 RNA_dep_RNAP]</span>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bso OCA], [http://pdbe.org/3bso PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bso RCSB], [http://www.ebi.ac.uk/pdbsum/3bso PDBsum]</span></td></tr>
|RELATEDENTRY=[[1sh0|1SH0]], [[3bsn|3BSN]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bso FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bso OCA], [http://www.ebi.ac.uk/pdbsum/3bso PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3bso RCSB]</span>
== Evolutionary Conservation ==
}}
[[Image:Consurf_key_small.gif|200px|right]]
 
Check<jmol>
'''Norwalk Virus polymerase bound to cytidine 5'-triphosphate and primer-template RNA'''
  <jmolCheckbox>
 
    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bs/3bso_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=3bso ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Crystal structures of Norwalk virus polymerase bound to an RNA primer-template duplex and either the natural substrate CTP or the inhibitor 5-nitrocytidine triphosphate have been determined to 1.8A resolution. These structures reveal a closed conformation of the polymerase that differs significantly from previously determined open structures of calicivirus and picornavirus polymerases. These closed complexes are trapped immediately prior to the nucleotidyl transfer reaction, with the triphosphate group of the nucleotide bound to two manganese ions at the active site, poised for reaction to the 3'-hydroxyl group of the RNA primer. The positioning of the 5-nitrocytidine triphosphate nitro group between the alpha-phosphate and the 3'-hydroxyl group of the primer suggests a novel, general approach for the design of antiviral compounds mimicking natural nucleosides and nucleotides.


==Overview==
Structural insights into mechanisms of catalysis and inhibition in Norwalk virus polymerase.,Zamyatkin DF, Parra F, Alonso JM, Harki DA, Peterson BR, Grochulski P, Ng KK J Biol Chem. 2008 Mar 21;283(12):7705-12. Epub 2008 Jan 9. PMID:18184655<ref>PMID:18184655</ref>
Crystal structures of Norwalk virus polymerase bound to an RNA primer-template duplex and either the natural substrate CTP or the inhibitor 5-nitrocytidine triphosphate have been determined to 1.8A resolution. These structures reveal a closed conformation of the polymerase that differs significantly from previously determined open structures of calicivirus and picornavirus polymerases. These closed complexes are trapped immediately prior to the nucleotidyl transfer reaction, with the triphosphate group of the nucleotide bound to two manganese ions at the active site, poised for reaction to the 3'-hydroxyl group of the RNA primer. The positioning of the 5-nitrocytidine triphosphate nitro group between the alpha-phosphate and the 3'-hydroxyl group of the primer suggests a novel, general approach for the design of antiviral compounds mimicking natural nucleosides and nucleotides.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
3BSO is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Norwalk_virus Norwalk virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BSO OCA].
</div>
<div class="pdbe-citations 3bso" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
Structural insights into mechanisms of catalysis and inhibition in norwalk virus polymerase., Zamyatkin DF, Parra F, Alonso JM, Harki DA, Peterson BR, Grochulski P, Ng KK, J Biol Chem. 2008 Mar 21;283(12):7705-12. Epub 2008 Jan 9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18184655 18184655]
*[[RNA polymerase|RNA polymerase]]
[[Category: Norwalk virus]]
== References ==
[[Category: Protein complex]]
<references/>
__TOC__
</StructureSection>
[[Category: Norwalk calicivirus]]
[[Category: RNA-directed RNA polymerase]]
[[Category: RNA-directed RNA polymerase]]
[[Category: Ng, K K.S.]]
[[Category: Ng, K K.S]]
[[Category: Zamyatkin, D F.]]
[[Category: Zamyatkin, D F]]
[[Category: antiviral enzyme inhibitor]]
[[Category: Antiviral enzyme inhibitor]]
[[Category: helicase]]
[[Category: Helicase]]
[[Category: hydrolase]]
[[Category: Hydrolase]]
[[Category: nucleotide-binding]]
[[Category: Nucleotide-binding]]
[[Category: nucleotidyltransferase]]
[[Category: Nucleotidyltransferase]]
[[Category: rna replication]]
[[Category: Rna replication]]
[[Category: rna-dependent rna polymerase]]
[[Category: Rna-dependent rna polymerase]]
[[Category: rna-directed rna polymerase]]
[[Category: Rna-directed rna polymerase]]
[[Category: transferase]]
[[Category: Transferase]]
[[Category: transferase/rna complex]]
[[Category: Transferase-rna complex]]
[[Category: viral replication]]
[[Category: Viral replication]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr  2 11:32:46 2008''

Latest revision as of 02:05, 10 February 2016

Norwalk Virus polymerase bound to cytidine 5'-triphosphate and primer-template RNA

3bso, resolution 1.74Å

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