2pus: Difference between revisions

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-[[Image:2pus.jpg|left|200px]]<br /><applet load="2pus" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2pus, resolution 2.40&Aring;" />
-'''Unprecedented activation mechanism of a non-canonical RNA-dependent RNA polymerase'''<br />
-==Overview==
+==Unprecedented activation mechanism of a non-canonical RNA-dependent RNA polymerase==
-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.
+<StructureSection load='2pus' size='340' side='right'caption='[[2pus]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2pus]] 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=2PUS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PUS 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]] 2.4&#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=2pus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pus OCA], [https://pdbe.org/2pus PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pus RCSB], [https://www.ebi.ac.uk/pdbsum/2pus PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pus ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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 ==
+[[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/pu/2pus_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=2pus ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-PUS is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://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=2PUS OCA].
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18077388 18077388]
 [[Category: Infectious bursal disease virus]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Abaitua, F.]]
+[[Category: Abaitua F]]
-[[Category: Garriga, D.]]
+[[Category: Garriga D]]
-[[Category: Navarro, A.]]
+[[Category: Navarro A]]
-[[Category: Querol-Audi, J.]]
+[[Category: Querol-Audi J]]
-[[Category: Rodriguez, J F.]]
+[[Category: Rodriguez JF]]
-[[Category: Verdaguer, N.]]
+[[Category: Verdaguer N]]
-[[Category: rna polymerase motifs]]
-[[Category: transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:33:14 2008''