1udq

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[[Image:1udq.png|left|200px]]
 
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{{STRUCTURE_1udq| PDB=1udq | SCENE= }}
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==Crystal structure of the tRNA processing enzyme RNase PH T125A mutant from Aquifex aeolicus==
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<StructureSection load='1udq' size='340' side='right'caption='[[1udq]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1udq]] is a 1 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=1UDQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UDQ FirstGlance]. <br>
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</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1udq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udq OCA], [https://pdbe.org/1udq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1udq RCSB], [https://www.ebi.ac.uk/pdbsum/1udq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1udq ProSAT], [https://www.topsan.org/Proteins/RSGI/1udq TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RNPH_AQUAE RNPH_AQUAE] 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 (By similarity).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ud/1udq_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1udq ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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RNase PH is one of the exoribonucleases that catalyze the 3' end processing of tRNA in bacteria. RNase PH removes nucleotides following the CCA sequence of tRNA precursors by phosphorolysis and generates mature tRNAs with amino acid acceptor activity. In this study, we determined the crystal structure of Aquifex aeolicus RNase PH bound with a phosphate, a co-substrate, in the active site at 2.3-A resolution. RNase PH has the typical alpha/beta fold, which forms a hexameric ring structure as a trimer of dimers. This ring structure resembles that of the polynucleotide phosphorylase core domain homotrimer, another phosphorolytic exoribonuclease. Four amino acid residues, Arg-86, Gly-124, Thr-125, and Arg-126, of RNase PH are involved in the phosphate-binding site. Mutational analyses of these residues showed their importance in the phosphorolysis reaction. A docking model with the tRNA acceptor stem suggests how RNase PH accommodates substrate RNAs.
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===Crystal structure of the tRNA processing enzyme RNase PH T125A mutant from Aquifex aeolicus===
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Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus.,Ishii R, Nureki O, Yokoyama S J Biol Chem. 2003 Aug 22;278(34):32397-404. Epub 2003 May 12. PMID:12746447<ref>PMID:12746447</ref>
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{{ABSTRACT_PUBMED_12746447}}
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==About this Structure==
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<div class="pdbe-citations 1udq" style="background-color:#fffaf0;"></div>
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[[1udq]] is a 1 chain structure of [[Ribonuclease]] with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UDQ OCA].
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==See Also==
==See Also==
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*[[Ribonuclease|Ribonuclease]]
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:012746447</ref><references group="xtra"/>
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__TOC__
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</StructureSection>
[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
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[[Category: TRNA nucleotidyltransferase]]
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[[Category: Large Structures]]
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[[Category: Ishii, R.]]
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[[Category: Ishii R]]
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[[Category: Nureki, O.]]
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[[Category: Nureki O]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Yokoyama S]]
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[[Category: Yokoyama, S.]]
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[[Category: Riken structural genomics/proteomics initiative]]
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[[Category: Rsgi]]
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[[Category: Structural genomic]]
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[[Category: Transferase]]
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Current revision

Crystal structure of the tRNA processing enzyme RNase PH T125A mutant from Aquifex aeolicus

PDB ID 1udq

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