1yyk: Difference between revisions

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-[[Image:1yyk.gif|left|200px]]<br /><applet load="1yyk" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1yyk, resolution 2.50&Aring;" />
-'''Crystal structure of RNase III from Aquifex Aeolicus complexed with double-stranded RNA at 2.5-angstrom resolution'''<br />
-==Overview==
+==Crystal structure of RNase III from Aquifex Aeolicus complexed with double-stranded RNA at 2.5-angstrom resolution==
-Bacterial ribonuclease III (RNase III) can affect RNA structure and gene, expression in either of two ways: as a processing enzyme that cleaves, double-stranded (ds) RNA, or as a binding protein that binds but does not, cleave dsRNA. We previously proposed a model of the catalytic complex of, RNase III with dsRNA based on three crystal structures, including the, endonuclease domain of RNase III with and without bound metal ions and a, dsRNA binding protein complexed with dsRNA. We also reported a, noncatalytic assembly observed in the crystal structure of an RNase III, mutant, which binds but does not cleave dsRNA, complexed with dsRNA. We, hypothesize that the RNase III*dsRNA complex can exist in two functional, forms, a catalytic complex and a noncatalytic assembly, and that in, between the two forms there may be intermediate states. Here, we present, four crystal structures of RNase III complexed with dsRNA, representing, possible intermediates.
+<StructureSection load='1yyk' size='340' side='right'caption='[[1yyk]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1yyk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YYK 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=1yyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yyk OCA], [https://pdbe.org/1yyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yyk RCSB], [https://www.ebi.ac.uk/pdbsum/1yyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yyk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNC_AQUAE RNC_AQUAE] Digests double-stranded RNA. Involved in the processing of primary rRNA transcript to yield the immediate precursors to the large and small rRNAs (23S and 16S). Also processes some mRNAs, and tRNAs when they are encoded in the rRNA operon.<ref>PMID:21138964</ref> <ref>PMID:16439209</ref>
+== 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/yy/1yyk_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=1yyk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Bacterial ribonuclease III (RNase III) can affect RNA structure and gene expression in either of two ways: as a processing enzyme that cleaves double-stranded (ds) RNA, or as a binding protein that binds but does not cleave dsRNA. We previously proposed a model of the catalytic complex of RNase III with dsRNA based on three crystal structures, including the endonuclease domain of RNase III with and without bound metal ions and a dsRNA binding protein complexed with dsRNA. We also reported a noncatalytic assembly observed in the crystal structure of an RNase III mutant, which binds but does not cleave dsRNA, complexed with dsRNA. We hypothesize that the RNase III*dsRNA complex can exist in two functional forms, a catalytic complex and a noncatalytic assembly, and that in between the two forms there may be intermediate states. Here, we present four crystal structures of RNase III complexed with dsRNA, representing possible intermediates.
-==About this Structure==
+Intermediate states of ribonuclease III in complex with double-stranded RNA.,Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X Structure. 2005 Oct;13(10):1435-42. PMID:16216575<ref>PMID:16216575</ref>
-YYK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus] with TRS as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Ribonuclease_III Ribonuclease III], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.3 3.1.26.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1YYK OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Intermediate states of ribonuclease III in complex with double-stranded RNA., Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X, Structure. 2005 Oct;13(10):1435-42. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16216575 16216575]
+</div>
+<div class="pdbe-citations 1yyk" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Aquifex aeolicus]]
-[[Category: Ribonuclease III]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Austin BP]]
-[[Category: Austin, B.P.]]
+[[Category: Court DL]]
-[[Category: Court, D.L.]]
+[[Category: Gan J]]
-[[Category: Gan, J.]]
+[[Category: Ji X]]
-[[Category: Ji, X.]]
+[[Category: Tropea JE]]
-[[Category: Tropea, J.E.]]
+[[Category: Waugh DS]]
-[[Category: Waugh, D.S.]]
-[[Category: TRS]]
-[[Category: double-stranded rna]]
-[[Category: endonucleolytic cleavage]]
-[[Category: ribonuclease iii]]
-[[Category: rna interference]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 07:08:05 2007''