1udn

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(New page: 200px<br /><applet load="1udn" size="450" color="white" frame="true" align="right" spinBox="true" caption="1udn, resolution 2.30&Aring;" /> '''Crystal structure of...)
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[[Image:1udn.jpg|left|200px]]<br /><applet load="1udn" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1udn, resolution 2.30&Aring;" />
 
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'''Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus'''<br />
 
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==Overview==
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==Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus==
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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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<StructureSection load='1udn' size='340' side='right'caption='[[1udn]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1udn]] 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=1UDN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UDN 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=1udn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udn OCA], [https://pdbe.org/1udn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1udn RCSB], [https://www.ebi.ac.uk/pdbsum/1udn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1udn ProSAT], [https://www.topsan.org/Proteins/RSGI/1udn 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/1udn_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=1udn 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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==About this Structure==
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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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1UDN 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 PO4 and SO4 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=1UDN OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12746447 12746447]
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</div>
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[[Category: Aquifex aeolicus]]
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<div class="pdbe-citations 1udn" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: tRNA nucleotidyltransferase]]
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[[Category: Ishii, R.]]
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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: PO4]]
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[[Category: SO4]]
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[[Category: riken structural genomics/proteomics initiative]]
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[[Category: rsgi]]
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[[Category: structural genomics]]
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[[Category: transferase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 04:02:50 2007''
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==See Also==
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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Aquifex aeolicus]]
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[[Category: Large Structures]]
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[[Category: Ishii R]]
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[[Category: Nureki O]]
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[[Category: Yokoyama S]]

Current revision

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

PDB ID 1udn

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