1udo

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[[Image:1udo.gif|left|200px]]
 
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{{Structure
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==Crystal structure of the tRNA processing enzyme RNase PH R86A mutant from Aquifex aeolicus==
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|PDB= 1udo |SIZE=350|CAPTION= <scene name='initialview01'>1udo</scene>, resolution 2.30&Aring;
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<StructureSection load='1udo' size='340' side='right'caption='[[1udo]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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<table><tr><td colspan='2'>[[1udo]] 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=1UDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UDO FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[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] </span>
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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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|GENE=
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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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|DOMAIN=
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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=1udo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udo OCA], [https://pdbe.org/1udo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1udo RCSB], [https://www.ebi.ac.uk/pdbsum/1udo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1udo ProSAT], [https://www.topsan.org/Proteins/RSGI/1udo TOPSAN]</span></td></tr>
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|RELATEDENTRY=[[1udn|1UDN]], [[1udq|1UDQ]], [[1uds|1UDS]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1udo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udo OCA], [http://www.ebi.ac.uk/pdbsum/1udo PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1udo RCSB]</span>
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== Function ==
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}}
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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/1udo_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=1udo 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 R86A 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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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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<div class="pdbe-citations 1udo" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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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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*[[Ribonuclease 3D structures|Ribonuclease 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1UDO is a [[Single protein]] structure of 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=1UDO OCA].
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__TOC__
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</StructureSection>
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==Reference==
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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://www.ncbi.nlm.nih.gov/pubmed/12746447 12746447]
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[[Category: Aquifex aeolicus]]
[[Category: Aquifex aeolicus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: tRNA nucleotidyltransferase]]
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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: Yokoyama S]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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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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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:08:51 2008''
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Current revision

Crystal structure of the tRNA processing enzyme RNase PH R86A mutant from Aquifex aeolicus

PDB ID 1udo

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