1oyr: Difference between revisions

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OCA

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-[[Image:1oyr.jpg|left|200px]]<br /><applet load="1oyr" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1oyr, resolution 3.10&Aring;" />
-'''Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis'''<br />
-==Overview==
+==Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis==
-RNase PH is a member of the family of phosphorolytic 3' --&gt; 5', exoribonucleases that also includes polynucleotide phosphorylase (PNPase)., RNase PH is involved in the maturation of tRNA precursors and especially, important for removal of nucleotide residues near the CCA acceptor end of, the mature tRNAs. Wild-type and triple mutant R68Q-R73Q-R76Q RNase PH from, Bacillus subtilis have been crystallized and the structures determined by, X-ray diffraction to medium resolution. Wild-type and triple mutant RNase, PH crystallize as a hexamer and dimer, respectively. The structures, contain a rare left-handed beta alpha beta-motif in the N-terminal portion, of the protein. This motif has also been identified in other enzymes, involved in RNA metabolism. The RNase PH structure and active site can, despite low sequence similarity, be overlayed with the N-terminal core of, the structure and active site of Streptomyces antibioticus PNPase. The, surface of the RNase PH dimer fit the shape of a tRNA molecule.
+<StructureSection load='1oyr' size='340' side='right'caption='[[1oyr]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1oyr]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OYR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OYR 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]] 3.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1oyr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oyr OCA], [https://pdbe.org/1oyr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oyr RCSB], [https://www.ebi.ac.uk/pdbsum/1oyr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oyr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RNPH_BACSU RNPH_BACSU] Phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates. Plays a role in the secondary pathway of 23S rRNA 3' end maturation.<ref>PMID:19880604</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/oy/1oyr_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=1oyr ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-OYR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with SO4 and CD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/tRNA_nucleotidyltransferase tRNA nucleotidyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.56 2.7.7.56] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1OYR OCA].
+*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
+== References ==
-==Reference==
+<references/>
-Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding., Harlow LS, Kadziola A, Jensen KF, Larsen S, Protein Sci. 2004 Mar;13(3):668-77. Epub 2004 Feb 6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14767080 14767080]
+__TOC__
+</StructureSection>
 [[Category: Bacillus subtilis]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: tRNA nucleotidyltransferase]]
+[[Category: Harlow LS]]
-[[Category: Harlow, L.S.]]
+[[Category: Jensen KF]]
-[[Category: Jensen, K.F.]]
+[[Category: Kadziola A]]
-[[Category: Kadziola, A.]]
+[[Category: Larsen S]]
-[[Category: Larsen, S.]]
-[[Category: CD]]
-[[Category: SO4]]
-[[Category: transferase]]
-[[Category: trna processing]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:18:22 2007''