2v9p: Difference between revisions

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-[[Image:2v9p.gif|left|200px]]<br /><applet load="2v9p" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2v9p, resolution 3.00&Aring;" />
-'''CRYSTAL STRUCTURE OF PAPILLOMAVIRUS E1 HEXAMERIC HELICASE DNA-FREE FORM'''<br />
-==Overview==
+==Crystal structure of papillomavirus E1 hexameric helicase DNA-free form==
-Concerted, stochastic and sequential mechanisms of action have been, proposed for different hexameric AAA+ molecular motors. Here we report the, crystal structure of the E1 helicase from bovine papillomavirus, where, asymmetric assembly is for the first time observed in the absence of, nucleotide cofactors and DNA. Surprisingly, the ATP-binding sites adopt, specific conformations linked to positional changes in the DNA-binding, hairpins, which follow a wave-like trajectory, as observed previously in, the E1/DNA/ADP complex. The protein's assembly thus maintains such an, asymmetric state in the absence of DNA and nucleotide cofactors, allowing, consideration of the E1 helicase action as the propagation of a, conformational wave around the protein ring. The data imply that the, wave's propagation within the AAA+ domains is not necessarily coupled with, a strictly sequential hydrolysis of ATP. Since a single ATP hydrolysis, event would affect the whole hexamer, such events may simply serve to, rectify the direction of the wave's motion.
+<StructureSection load='2v9p' size='340' side='right'caption='[[2v9p]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2v9p]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Deltapapillomavirus_4 Deltapapillomavirus 4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V9P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V9P 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]] 3&#8491;</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>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=2v9p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v9p OCA], [https://pdbe.org/2v9p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v9p RCSB], [https://www.ebi.ac.uk/pdbsum/2v9p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v9p ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/VE1_BPV1 VE1_BPV1] ATP-dependent DNA helicase required for initiation of viral DNA replication. It forms a complex with the viral E2 protein. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins.
+== 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/v9/2v9p_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=2v9p ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Concerted, stochastic and sequential mechanisms of action have been proposed for different hexameric AAA+ molecular motors. Here we report the crystal structure of the E1 helicase from bovine papillomavirus, where asymmetric assembly is for the first time observed in the absence of nucleotide cofactors and DNA. Surprisingly, the ATP-binding sites adopt specific conformations linked to positional changes in the DNA-binding hairpins, which follow a wave-like trajectory, as observed previously in the E1/DNA/ADP complex. The protein's assembly thus maintains such an asymmetric state in the absence of DNA and nucleotide cofactors, allowing consideration of the E1 helicase action as the propagation of a conformational wave around the protein ring. The data imply that the wave's propagation within the AAA+ domains is not necessarily coupled with a strictly sequential hydrolysis of ATP. Since a single ATP hydrolysis event would affect the whole hexamer, such events may simply serve to rectify the direction of the wave's motion.
-==About this Structure==
+Papillomavirus E1 helicase assembly maintains an asymmetric state in the absence of DNA and nucleotide cofactors.,Sanders CM, Kovalevskiy OV, Sizov D, Lebedev AA, Isupov MN, Antson AA Nucleic Acids Res. 2007;35(19):6451-7. Epub 2007 Sep 19. PMID:17881379<ref>PMID:17881379</ref>
-V9P is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bovine_papillomavirus_type_2 Bovine papillomavirus type 2] with <scene name='pdbligand=PO4:'>PO4</scene> and <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Sites: <scene name='pdbsite=AC1:Po4 Binding Site For Chain A'>AC1</scene>, <scene name='pdbsite=AC2:Po4 Binding Site For Chain A'>AC2</scene>, <scene name='pdbsite=AC3:Mg Binding Site For Chain A'>AC3</scene>, <scene name='pdbsite=AC4:Po4 Binding Site For Chain B'>AC4</scene>, <scene name='pdbsite=AC5:Po4 Binding Site For Chain B'>AC5</scene>, <scene name='pdbsite=AC6:Mg Binding Site For Chain B'>AC6</scene>, <scene name='pdbsite=AC7:Po4 Binding Site For Chain C'>AC7</scene>, <scene name='pdbsite=AC8:Po4 Binding Site For Chain C'>AC8</scene>, <scene name='pdbsite=AC9:Mg Binding Site For Chain C'>AC9</scene>, <scene name='pdbsite=BC1:Po4 Binding Site For Chain D'>BC1</scene>, <scene name='pdbsite=BC2:Po4 Binding Site For Chain E'>BC2</scene>, <scene name='pdbsite=BC3:Po4 Binding Site For Chain F'>BC3</scene>, <scene name='pdbsite=BC4:Po4 Binding Site For Chain G'>BC4</scene>, <scene name='pdbsite=BC5:Po4 Binding Site For Chain G'>BC5</scene>, <scene name='pdbsite=BC6:Mg Binding Site For Chain G'>BC6</scene>, <scene name='pdbsite=BC7:Po4 Binding Site For Chain H'>BC7</scene>, <scene name='pdbsite=BC8:Po4 Binding Site For Chain H'>BC8</scene>, <scene name='pdbsite=BC9:Mg Binding Site For Chain H'>BC9</scene>, <scene name='pdbsite=CC1:Po4 Binding Site For Chain I'>CC1</scene>, <scene name='pdbsite=CC2:Po4 Binding Site For Chain I'>CC2</scene>, <scene name='pdbsite=CC3:Mg Binding Site For Chain I'>CC3</scene>, <scene name='pdbsite=CC4:Po4 Binding Site For Chain J'>CC4</scene>, <scene name='pdbsite=CC5:Po4 Binding Site For Chain K'>CC5</scene> and <scene name='pdbsite=CC6:Po4 Binding Site For Chain L'>CC6</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V9P OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Papillomavirus E1 helicase assembly maintains an asymmetric state in the absence of DNA and nucleotide cofactors., Sanders CM, Kovalevskiy OV, Sizov D, Lebedev AA, Isupov MN, Antson AA, Nucleic Acids Res. 2007 Sep 19;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17881379 17881379]
+</div>
-[[Category: Bovine papillomavirus type 2]]
+<div class="pdbe-citations 2v9p" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
-[[Category: Antson, A.A.]]
-[[Category: Isupov, M.N.]]
-[[Category: Kovalevskiy, O.V.]]
-[[Category: Lebedev, A.A.]]
-[[Category: Sanders, C.M.]]
-[[Category: Sizov, D.]]
-[[Category: MG]]
-[[Category: PO4]]
-[[Category: aaa+ molecular motor]]
-[[Category: atp-binding]]
-[[Category: atpase]]
-[[Category: dna replication]]
-[[Category: dna translocation]]
-[[Category: dna-binding]]
-[[Category: early protein]]
-[[Category: helicase]]
-[[Category: hydrolase]]
-[[Category: nucleotide-binding]]
-[[Category: nucleus]]
-[[Category: replication]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 12:07:29 2008''
+==See Also==
+*[[Helicase 3D structures|Helicase 3D structures]]
+*[[Replication protein E1|Replication protein E1]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Deltapapillomavirus 4]]
+[[Category: Large Structures]]
+[[Category: Antson AA]]
+[[Category: Isupov MN]]
+[[Category: Kovalevskiy OV]]
+[[Category: Lebedev AA]]
+[[Category: Sanders CM]]
+[[Category: Sizov D]]