3bsn
From Proteopedia
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{{Structure | {{Structure | ||
|PDB= 3bsn |SIZE=350|CAPTION= <scene name='initialview01'>3bsn</scene>, resolution 1.80Å | |PDB= 3bsn |SIZE=350|CAPTION= <scene name='initialview01'>3bsn</scene>, resolution 1.80Å | ||
| - | |SITE= | + | |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:N5c+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> |
|LIGAND= <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=N5C:5-NITROCYTIDINE+5'-(TETRAHYDROGEN+TRIPHOSPHATE)'>N5C</scene>, <scene name='pdbligand=N5M:5-NITROCYTIDINE+5'-(DIHYDROGEN+PHOSPHATE)'>N5M</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> | |LIGAND= <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=N5C:5-NITROCYTIDINE+5'-(TETRAHYDROGEN+TRIPHOSPHATE)'>N5C</scene>, <scene name='pdbligand=N5M:5-NITROCYTIDINE+5'-(DIHYDROGEN+PHOSPHATE)'>N5M</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene> | ||
|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> | |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> | ||
|GENE= | |GENE= | ||
| - | |DOMAIN= | + | |DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd01699 RNA_dep_RNAP]</span> |
|RELATEDENTRY=[[1sh0|1SH0]], [[3bso|3BSO]] | |RELATEDENTRY=[[1sh0|1SH0]], [[3bso|3BSO]] | ||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bsn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bsn OCA], [http://www.ebi.ac.uk/pdbsum/3bsn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3bsn RCSB]</span> | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bsn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bsn OCA], [http://www.ebi.ac.uk/pdbsum/3bsn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3bsn RCSB]</span> | ||
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'''Norwalk Virus polymerase bound to 5-nitrocytidine triphosphate and primer-template RNA''' | '''Norwalk Virus polymerase bound to 5-nitrocytidine triphosphate and primer-template RNA''' | ||
| + | |||
| + | ==Overview== | ||
| + | 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== | ==About this Structure== | ||
3BSN 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=3BSN OCA]. | 3BSN 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=3BSN OCA]. | ||
| + | |||
| + | ==Reference== | ||
| + | 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] | ||
[[Category: Norwalk virus]] | [[Category: Norwalk virus]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
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[[Category: viral replication]] | [[Category: viral replication]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 2 11:32:43 2008'' |
Revision as of 08:32, 2 April 2008
| |||||||
| , resolution 1.80Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , , , , , and | ||||||
| Ligands: | , , , , , , | ||||||
| Activity: | RNA-directed RNA polymerase, with EC number 2.7.7.48 | ||||||
| Domains: | RNA_dep_RNAP | ||||||
| Related: | 1SH0, 3BSO
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Norwalk Virus polymerase bound to 5-nitrocytidine triphosphate and primer-template RNA
Overview
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
3BSN is a Protein complex structure of sequences from Norwalk virus. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Wed Apr 2 11:32:43 2008
Categories: Norwalk virus | Protein complex | RNA-directed RNA polymerase | Ng, K K.S. | Zamyatkin, D F. | Antiviral enzyme inhibitor | Helicase | Hydrolase | Nucleotide-binding | Nucleotidyltransferase | Rna replication | Rna-dependent rna polymerase | Rna-directed rna polymerase | Transferase | Transferase/rna complex | Viral replication
