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| | ==Crystal structure of infectious bursal disease virus VP1 polymerase, incubated with Mg2+ ion.== | | ==Crystal structure of infectious bursal disease virus VP1 polymerase, incubated with Mg2+ ion.== |
| - | <StructureSection load='2r72' size='340' side='right' caption='[[2r72]], [[Resolution|resolution]] 3.15Å' scene=''> | + | <StructureSection load='2r72' size='340' side='right'caption='[[2r72]], [[Resolution|resolution]] 3.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2r72]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Avian_infectious_bursal_disease_virus Avian infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R72 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2R72 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2r72]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Infectious_bursal_disease_virus Infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R72 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R72 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.15Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2pus|2pus]], [[2r70|2r70]], [[2qj1|2qj1]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VP1 polymerase (segment B) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10995 Avian infectious bursal disease virus])</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=2r72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r72 OCA], [https://pdbe.org/2r72 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r72 RCSB], [https://www.ebi.ac.uk/pdbsum/2r72 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r72 ProSAT]</span></td></tr> |
| - | <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=2r72 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r72 OCA], [http://pdbe.org/2r72 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2r72 RCSB], [http://www.ebi.ac.uk/pdbsum/2r72 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2r72 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RDRP_IBDV RDRP_IBDV]] RNA-dependent RNA polymerase which is found both free and covalently attached to the genomic RNA. May also contain guanylyl and methyl transferase activities (By similarity). | + | [https://www.uniprot.org/uniprot/RDRP_IBDV RDRP_IBDV] RNA-dependent RNA polymerase which is found both free and covalently attached to the genomic RNA. May also contain guanylyl and methyl transferase activities (By similarity). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Avian infectious bursal disease virus]] | |
| - | [[Category: Abaitua, F]] | |
| - | [[Category: Garriga, D]] | |
| - | [[Category: Navarro, A]] | |
| - | [[Category: Querol-Audi, J]] | |
| - | [[Category: Rodriguez, J F]] | |
| - | [[Category: Verdaguer, N]] | |
| - | [[Category: Birnavirus]] | |
| - | [[Category: Ibdv]] | |
| | [[Category: Infectious bursal disease virus]] | | [[Category: Infectious bursal disease virus]] |
| - | [[Category: Magnesium]] | + | [[Category: Large Structures]] |
| - | [[Category: Mg]] | + | [[Category: Abaitua F]] |
| - | [[Category: Polymerase]] | + | [[Category: Garriga D]] |
| - | [[Category: Transferase]] | + | [[Category: Navarro A]] |
| - | [[Category: Vp1]] | + | [[Category: Querol-Audi J]] |
| | + | [[Category: Rodriguez JF]] |
| | + | [[Category: Verdaguer N]] |
| Structural highlights
Function
RDRP_IBDV RNA-dependent RNA polymerase which is found both free and covalently attached to the genomic RNA. May also contain guanylyl and methyl transferase activities (By similarity).
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Two lineages of viral RNA-dependent RNA polymerases (RDRPs) differing in the organization (canonical vs. noncanonical) of the palm subdomain have been identified. Phylogenetic analyses indicate that both lineages diverged at a very early stage of the evolution of the enzyme [Gorbalenya AE, Pringle FM, Zeddam JL, Luke BT, Cameron CE, Kalmakoff J, Hanzlik TN, Gordon KH, Ward VK (2002) J Mol Biol 324:47-62]. Here, we report the x-ray structure of a noncanonical birnaviral RDRP, named VP1, in its free form, bound to Mg(2+) ions, and bound to a peptide representing the polymerase-binding motif of the regulatory viral protein VP3. The structure of VP1 reveals that the noncanonical connectivity of the palm subdomain maintains the geometry of the catalytic residues found in canonical polymerases but results in a partial blocking of the active site cavity. The VP1-VP3 peptide complex shows a mode of polymerase activation in which VP3 binding promotes a conformational change that removes the steric blockade of the VP1 active site, facilitating the accommodation of the template and incoming nucleotides for catalysis. The striking structural similarities between birnavirus (dsRNA) and the positive-stranded RNA picornavirus and calicivirus RDRPs provide evidence supporting the existence of functional and evolutionary relationships between these two virus groups.
Activation mechanism of a noncanonical RNA-dependent RNA polymerase.,Garriga D, Navarro A, Querol-Audi J, Abaitua F, Rodriguez JF, Verdaguer N Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20540-5. Epub 2007 Dec 11. PMID:18077388[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Garriga D, Navarro A, Querol-Audi J, Abaitua F, Rodriguez JF, Verdaguer N. Activation mechanism of a noncanonical RNA-dependent RNA polymerase. Proc Natl Acad Sci U S A. 2007 Dec 18;104(51):20540-5. Epub 2007 Dec 11. PMID:18077388
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