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New page: left|200px<br /><applet load="1yvu" size="450" color="white" frame="true" align="right" spinBox="true" caption="1yvu, resolution 2.90Å" /> '''Crystal structure of...
 
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[[Image:1yvu.gif|left|200px]]<br /><applet load="1yvu" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1yvu, resolution 2.90&Aring;" />
'''Crystal structure of A. aeolicus Argonaute'''<br />


==Overview==
==Crystal structure of A. aeolicus Argonaute==
Argonaute (Ago) proteins constitute a key component of the RNA-induced, silencing complex (RISC). We report the crystal structure of Aquifex, aeolicus Ago (Aa-Ago) together with binding and cleavage studies, which, establish this eubacterial Ago as a bona fide guide DNA strand-mediated, site-specific RNA endonuclease. We have generated a stereochemically, robust model of the complex, where the guide DNA-mRNA duplex is positioned, within a basic channel spanning the bilobal interface, such that the 5', phosphate of the guide strand can be anchored in a basic pocket, and the, mRNA can be positioned for site-specific cleavage by RNase H-type divalent, cation-coordinated catalytic Asp residues of the PIWI domain. Domain swap, experiments involving chimeras of human Ago (hAgo1) and cleavage-competent, hAgo2 reinforce the role of the PIWI domain in "slicer" activity. We, propose a four-step Ago-mediated catalytic cleavage cycle model, which, provides distinct perspectives into the mechanism of guide strand-mediated, mRNA cleavage within the RISC.
<StructureSection load='1yvu' size='340' side='right'caption='[[1yvu]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1yvu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus_VF5 Aquifex aeolicus VF5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YVU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YVU 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]] 2.9&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1yvu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yvu OCA], [https://pdbe.org/1yvu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yvu RCSB], [https://www.ebi.ac.uk/pdbsum/1yvu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yvu ProSAT]</span></td></tr>
</table>
== 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/yv/1yvu_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1yvu ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Argonaute (Ago) proteins constitute a key component of the RNA-induced silencing complex (RISC). We report the crystal structure of Aquifex aeolicus Ago (Aa-Ago) together with binding and cleavage studies, which establish this eubacterial Ago as a bona fide guide DNA strand-mediated site-specific RNA endonuclease. We have generated a stereochemically robust model of the complex, where the guide DNA-mRNA duplex is positioned within a basic channel spanning the bilobal interface, such that the 5' phosphate of the guide strand can be anchored in a basic pocket, and the mRNA can be positioned for site-specific cleavage by RNase H-type divalent cation-coordinated catalytic Asp residues of the PIWI domain. Domain swap experiments involving chimeras of human Ago (hAgo1) and cleavage-competent hAgo2 reinforce the role of the PIWI domain in "slicer" activity. We propose a four-step Ago-mediated catalytic cleavage cycle model, which provides distinct perspectives into the mechanism of guide strand-mediated mRNA cleavage within the RISC.


==About this Structure==
Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage.,Yuan YR, Pei Y, Ma JB, Kuryavyi V, Zhadina M, Meister G, Chen HY, Dauter Z, Tuschl T, Patel DJ Mol Cell. 2005 Aug 5;19(3):405-19. PMID:16061186<ref>PMID:16061186</ref>
1YVU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus_vf5 Aquifex aeolicus vf5] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YVU OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage., Yuan YR, Pei Y, Ma JB, Kuryavyi V, Zhadina M, Meister G, Chen HY, Dauter Z, Tuschl T, Patel DJ, Mol Cell. 2005 Aug 5;19(3):405-19. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16061186 16061186]
</div>
[[Category: Aquifex aeolicus vf5]]
<div class="pdbe-citations 1yvu" style="background-color:#fffaf0;"></div>
[[Category: Single protein]]
== References ==
[[Category: Chen, H.Y.]]
<references/>
[[Category: Dauter, Z.]]
__TOC__
[[Category: Kuryavyi, V.]]
</StructureSection>
[[Category: Ma, J.B.]]
[[Category: Aquifex aeolicus VF5]]
[[Category: Meister, G.]]
[[Category: Large Structures]]
[[Category: Patel, D.J.]]
[[Category: Chen HY]]
[[Category: Pei, Y.]]
[[Category: Dauter Z]]
[[Category: Tuschl, T.]]
[[Category: Kuryavyi V]]
[[Category: Yuan, Y.R.]]
[[Category: Ma JB]]
[[Category: Zhadina, M.]]
[[Category: Meister G]]
[[Category: CA]]
[[Category: Patel DJ]]
[[Category: rnase h fold]]
[[Category: Pei Y]]
 
[[Category: Tuschl T]]
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 04:36:36 2007''
[[Category: Yuan YR]]
[[Category: Zhadina M]]
Retrieved from "https://proteopedia.org/1yvu"