1j3l: Difference between revisions

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-[[Image:1j3l.gif|left|200px]]<br /><applet load="1j3l" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1j3l, resolution 2.30&Aring;" />
-'''Structure of the RNA-processing inhibitor RraA from Thermus thermophilis'''<br />
-==Overview==
+==Structure of the RNA-processing inhibitor RraA from Thermus thermophilis==
-The menG gene product, thought to catalyze the final methylation in, vitamin K(2) synthesis, has recently been shown to inhibit RNase E in, Eschericha coli. The structure of the protein, since renamed RraA, has, been solved to 2.3 A using the multiple-wavelength anomalous diffraction, method and selenomethionine-substituted protein from Thermus thermophilus., The six molecules in the asymmetric unit are arranged as two similar, trimers which have a degree of interaction, suggesting biological, significance. The fold does not support the postulated methylation, function. Genomic analysis, specifically a lack of an RNase E homologue in, cases where homologues to RraA exist, indicates that the function is still, obscure.
+<StructureSection load='1j3l' size='340' side='right'caption='[[1j3l]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1j3l]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J3L 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]] 2.3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1j3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j3l OCA], [https://pdbe.org/1j3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j3l RCSB], [https://www.ebi.ac.uk/pdbsum/1j3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j3l ProSAT], [https://www.topsan.org/Proteins/RSGI/1j3l TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RRAAH_THET8 RRAAH_THET8] Catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2-oxoglutarate (HMG) into 2 molecules of pyruvate. Also contains a secondary oxaloacetate (OAA) decarboxylase activity due to the common pyruvate enolate transition state formed following C-C bond cleavage in the retro-aldol and decarboxylation reactions.<ref>PMID:24359411</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/j3/1j3l_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=1j3l ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The menG gene product, thought to catalyze the final methylation in vitamin K(2) synthesis, has recently been shown to inhibit RNase E in Eschericha coli. The structure of the protein, since renamed RraA, has been solved to 2.3 A using the multiple-wavelength anomalous diffraction method and selenomethionine-substituted protein from Thermus thermophilus. The six molecules in the asymmetric unit are arranged as two similar trimers which have a degree of interaction, suggesting biological significance. The fold does not support the postulated methylation function. Genomic analysis, specifically a lack of an RNase E homologue in cases where homologues to RraA exist, indicates that the function is still obscure.
-==About this Structure==
+Structure of the RNA-processing inhibitor RraA from Thermus thermophilis.,Rehse PH, Kuroishi C, Tahirov TH Acta Crystallogr D Biol Crystallogr. 2004 Nov;60(Pt 11):1997-2002. Epub, 2004 Oct 20. PMID:15502308<ref>PMID:15502308</ref>
-J3L is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with MG and CL as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1J3L OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structure of the RNA-processing inhibitor RraA from Thermus thermophilis., Rehse PH, Kuroishi C, Tahirov TH, Acta Crystallogr D Biol Crystallogr. 2004 Nov;60(Pt 11):1997-2002. Epub, 2004 Oct 20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15502308 15502308]
+</div>
-[[Category: Single protein]]
+<div class="pdbe-citations 1j3l" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermus thermophilus]]
-[[Category: Miyano, M.]]
+[[Category: Miyano M]]
-[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
+[[Category: Rehse PH]]
-[[Category: Rehse, P.H.]]
+[[Category: Tahirov TH]]
-[[Category: Tahirov, T.H.]]
-[[Category: CL]]
-[[Category: MG]]
-[[Category: riken structural genomics/proteomics initiative]]
-[[Category: rsgi]]
-[[Category: structural genomics]]
-[[Category: vitamine k2]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:02:42 2007''