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2pgg

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[[Image:2pgg.gif|left|200px]]
 
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==Crystal Structure of a Birnavirus (IBDV) RNA-dependent RNA Polymerase VP1==
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The line below this paragraph, containing "STRUCTURE_2pgg", creates the "Structure Box" on the page.
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<StructureSection load='2pgg' size='340' side='right'caption='[[2pgg]], [[Resolution|resolution]] 2.50&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'>[[2pgg]] 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=2PGG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PGG FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.5&#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=2pgg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pgg OCA], [https://pdbe.org/2pgg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pgg RCSB], [https://www.ebi.ac.uk/pdbsum/2pgg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pgg ProSAT]</span></td></tr>
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{{STRUCTURE_2pgg| PDB=2pgg | SCENE= }}
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</table>
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== Function ==
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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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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pg/2pgg_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2pgg ConSurf].
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<div style="clear:both"></div>
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'''Crystal Structure of a Birnavirus (IBDV) RNA-dependent RNA Polymerase VP1'''
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==See Also==
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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Single-subunit polymerases are universally encoded in both cellular organisms and viruses. Their three-dimensional structures have the shape of a right-hand with the active site located in the palm region, which has a topology similar to that of the RNA recognition motif (RRM) found in many RNA-binding proteins. Considering that polymerases have well conserved structures, it was surprising that the RNA-dependent RNA polymerases from birnaviruses, a group of dsRNA viruses, have their catalytic motifs arranged in a permuted order in sequence. Here we report the 2.5 A structure of a birnavirus VP1 in which the polymerase palm subdomain adopts a new active site topology that has not been previously observed in other polymerases. In addition, the polymerase motif C of VP1 has the sequence of -ADN-, a highly unusual feature for RNA-dependent polymerases. Through site-directed mutagenesis, we have shown that changing the VP1 motif C from -ADN- to -GDD- results in a mutant with an increased RNA synthesis activity. Our results indicate that the active site topology of VP1 may represent a newly developed branch in polymerase evolution, and that birnaviruses may have acquired the -ADN- mutation to control their growth rate.
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==About this Structure==
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2PGG is a [[Single protein]] structure of sequence 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=2PGG OCA].
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==Reference==
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The structure of a birnavirus polymerase reveals a distinct active site topology., Pan J, Vakharia VN, Tao YJ, Proc Natl Acad Sci U S A. 2007 May 1;104(18):7385-90. Epub 2007 Apr 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17456597 17456597]
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[[Category: Infectious bursal disease virus]]
[[Category: Infectious bursal disease virus]]
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[[Category: RNA-directed RNA polymerase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Pan J]]
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[[Category: Pan, J.]]
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[[Category: Tao YJ]]
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[[Category: Tao, Y J.]]
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[[Category: Vakharia VN]]
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[[Category: Vakharia, V N.]]
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[[Category: Birnavirus]]
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[[Category: Dsrna virus]]
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[[Category: Ibdv]]
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[[Category: Permutation]]
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[[Category: Polymerase]]
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[[Category: Rdrp]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 13:03:47 2008''
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Current revision

Crystal Structure of a Birnavirus (IBDV) RNA-dependent RNA Polymerase VP1

PDB ID 2pgg

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