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New page: left|200px<br /><applet load="2pgg" size="450" color="white" frame="true" align="right" spinBox="true" caption="2pgg, resolution 2.50Å" /> '''Crystal Structure of...
 
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[[Image:2pgg.gif|left|200px]]<br /><applet load="2pgg" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2pgg, resolution 2.50&Aring;" />
'''Crystal Structure of a Birnavirus (IBDV) RNA-dependent RNA Polymerase VP1'''<br />


==Overview==
==Crystal Structure of a Birnavirus (IBDV) RNA-dependent RNA Polymerase VP1==
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.
<StructureSection load='2pgg' size='340' side='right'caption='[[2pgg]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<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>
</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>
<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>
</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/pg/2pgg_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=2pgg ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2PGG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Infectious_bursal_disease_virus Infectious bursal disease virus]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2PGG OCA].
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17456597 17456597]
[[Category: Infectious bursal disease virus]]
[[Category: Infectious bursal disease virus]]
[[Category: RNA-directed RNA polymerase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Pan J]]
[[Category: Pan, J.]]
[[Category: Tao YJ]]
[[Category: Tao, Y.J.]]
[[Category: Vakharia VN]]
[[Category: Vakharia, V.N.]]
[[Category: birnavirus]]
[[Category: dsrna virus]]
[[Category: ibdv]]
[[Category: permutation]]
[[Category: polymerase]]
[[Category: rdrp]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:31:37 2007''

Latest revision as of 09:09, 21 February 2024

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

2pgg, resolution 2.50Å

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