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New page: left|200px<br /><applet load="2gjw" size="450" color="white" frame="true" align="right" spinBox="true" caption="2gjw, resolution 2.85Å" /> '''RNA Recognition and ...
 
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[[Image:2gjw.gif|left|200px]]<br /><applet load="2gjw" size="450" color="white" frame="true" align="right" spinBox="true"
caption="2gjw, resolution 2.85&Aring;" />
'''RNA Recognition and Cleavage by an Splicing Endonuclease'''<br />


==Overview==
==RNA Recognition and Cleavage by an Splicing Endonuclease==
The RNA splicing endonuclease cleaves two phosphodiester bonds within, folded precursor RNAs during intron removal, producing the functional RNAs, required for protein synthesis. Here we describe at a resolution of 2.85, angstroms the structure of a splicing endonuclease from Archaeglobus, fulgidus bound with a bulge-helix-bulge RNA containing a noncleaved and a, cleaved splice site. The endonuclease dimer cooperatively recognized a, flipped-out bulge base and stabilizes sharply bent bulge backbones that, are poised for an in-line RNA cleavage reaction. Cooperativity arises, because an arginine pair from one catalytic domain sandwiches a nucleobase, within the bulge cleaved by the other catalytic domain.
<StructureSection load='2gjw' size='340' side='right'caption='[[2gjw]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2gjw]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GJW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GJW 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]] 2.85&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A23:ADENOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>A23</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=2gjw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gjw OCA], [https://pdbe.org/2gjw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gjw RCSB], [https://www.ebi.ac.uk/pdbsum/2gjw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gjw ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ENDA_ARCFU ENDA_ARCFU] Endonuclease that removes tRNA introns. Cleaves pre-tRNA at the 5'- and 3'-splice sites to release the intron. The products are an intron and two tRNA half-molecules bearing 2',3' cyclic phosphate and 5'-OH termini. Recognizes a pseudosymmetric substrate in which 2 bulged loops of 3 bases are separated by a stem of 4 bp.
== 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/gj/2gjw_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=2gjw ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The RNA splicing endonuclease cleaves two phosphodiester bonds within folded precursor RNAs during intron removal, producing the functional RNAs required for protein synthesis. Here we describe at a resolution of 2.85 angstroms the structure of a splicing endonuclease from Archaeglobus fulgidus bound with a bulge-helix-bulge RNA containing a noncleaved and a cleaved splice site. The endonuclease dimer cooperatively recognized a flipped-out bulge base and stabilizes sharply bent bulge backbones that are poised for an in-line RNA cleavage reaction. Cooperativity arises because an arginine pair from one catalytic domain sandwiches a nucleobase within the bulge cleaved by the other catalytic domain.


==About this Structure==
RNA recognition and cleavage by a splicing endonuclease.,Xue S, Calvin K, Li H Science. 2006 May 12;312(5775):906-10. PMID:16690865<ref>PMID:16690865</ref>
2GJW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Active as [http://en.wikipedia.org/wiki/tRNA-intron_endonuclease tRNA-intron endonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.27.9 3.1.27.9] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2GJW OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
RNA recognition and cleavage by a splicing endonuclease., Xue S, Calvin K, Li H, Science. 2006 May 12;312(5775):906-10. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16690865 16690865]
</div>
<div class="pdbe-citations 2gjw" style="background-color:#fffaf0;"></div>
 
==See Also==
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Archaeoglobus fulgidus]]
[[Category: Archaeoglobus fulgidus]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: tRNA-intron endonuclease]]
[[Category: Calvin K]]
[[Category: Calvin, K.]]
[[Category: Li H]]
[[Category: Li, H.]]
[[Category: Xue S]]
[[Category: Xue, S.]]
[[Category: bulge-helix-bulge rna-protein complex]]
[[Category: splicing endonuclease af]]
 
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