2r70

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[[Image:2r70.jpg|left|200px]]
 
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==Crystal structure of infectious bursal disease virus VP1 polymerase, cocrystallized with an oligopeptide mimicking the VP3 C-terminus.==
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The line below this paragraph, containing "STRUCTURE_2r70", creates the "Structure Box" on the page.
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<StructureSection load='2r70' size='340' side='right'caption='[[2r70]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2r70]] 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=2R70 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R70 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2r70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r70 OCA], [https://pdbe.org/2r70 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r70 RCSB], [https://www.ebi.ac.uk/pdbsum/2r70 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r70 ProSAT]</span></td></tr>
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{{STRUCTURE_2r70| PDB=2r70 | SCENE= }}
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</table>
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== Function ==
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'''Crystal structure of infectious bursal disease virus VP1 polymerase, cocrystallized with an oligopeptide mimicking the VP3 C-terminus.'''
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[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).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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==Overview==
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Check<jmol>
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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.
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r7/2r70_consurf.spt"</scriptWhenChecked>
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==About this Structure==
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R70 OCA].
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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==Reference==
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</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=2r70 ConSurf].
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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://www.ncbi.nlm.nih.gov/pubmed/18077388 18077388]
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<div style="clear:both"></div>
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[[Category: Abaitua, F.]]
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__TOC__
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[[Category: Garriga, D.]]
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</StructureSection>
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[[Category: Navarro, A.]]
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[[Category: Querol-Audi, J.]]
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[[Category: Rodriguez, J F.]]
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[[Category: Verdaguer, N.]]
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[[Category: Activation]]
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[[Category: Birnavirus]]
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[[Category: Ibdv]]
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[[Category: Infectious bursal disease virus]]
[[Category: Infectious bursal disease virus]]
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[[Category: Polymerase]]
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[[Category: Large Structures]]
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[[Category: Transferase]]
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[[Category: Abaitua F]]
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[[Category: Vp1]]
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[[Category: Garriga D]]
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[[Category: Vp3]]
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[[Category: Navarro A]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 16:21:38 2008''
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[[Category: Querol-Audi J]]
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[[Category: Rodriguez JF]]
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[[Category: Verdaguer N]]

Current revision

Crystal structure of infectious bursal disease virus VP1 polymerase, cocrystallized with an oligopeptide mimicking the VP3 C-terminus.

PDB ID 2r70

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