1uds

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[[Image:1uds.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of the tRNA processing enzyme RNase PH R126A mutant from Aquifex aeolicus==
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|PDB= 1uds |SIZE=350|CAPTION= <scene name='initialview01'>1uds</scene>, resolution 2.30&Aring;
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<StructureSection load='1uds' size='340' side='right'caption='[[1uds]], [[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> and <scene name='pdbligand=SO4:SULFATE ION'>SO4</scene>
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<table><tr><td colspan='2'>[[1uds]] 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=1UDS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UDS FirstGlance]. <br>
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|ACTIVITY= [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]
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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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}}
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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=1uds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uds OCA], [https://pdbe.org/1uds PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uds RCSB], [https://www.ebi.ac.uk/pdbsum/1uds PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uds ProSAT], [https://www.topsan.org/Proteins/RSGI/1uds 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/1uds_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=1uds 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 R126A 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 1uds" 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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1UDS 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=1UDS 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: 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 genomic]]
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[[Category: transferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:30:41 2008''
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Current revision

Crystal structure of the tRNA processing enzyme RNase PH R126A mutant from Aquifex aeolicus

PDB ID 1uds

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