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| | ==Crystal structure of the tRNA processing enzyme RNase PH R86A mutant from Aquifex aeolicus== | | ==Crystal structure of the tRNA processing enzyme RNase PH R86A mutant from Aquifex aeolicus== |
| - | <StructureSection load='1udo' size='340' side='right' caption='[[1udo]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='1udo' size='340' side='right'caption='[[1udo]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1udo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UDO FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1udn|1udn]], [[1udq|1udq]], [[1uds|1uds]]</td></tr> | + | <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> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></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=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> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><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://pdbe.org/1udo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1udo RCSB], [http://www.ebi.ac.uk/pdbsum/1udo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1udo ProSAT], [http://www.topsan.org/Proteins/RSGI/1udo TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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). | + | [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). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Ribonuclease|Ribonuclease]] | + | *[[Ribonuclease 3D structures|Ribonuclease 3D structures]] |
| - | *[[Temp|Temp]]
| + | |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aquifex aeolicus huber and stetter 2001]] | + | [[Category: Aquifex aeolicus]] |
| - | [[Category: TRNA nucleotidyltransferase]] | + | [[Category: Large Structures]] |
| - | [[Category: Ishii, R]] | + | [[Category: Ishii R]] |
| - | [[Category: Nureki, O]] | + | [[Category: Nureki O]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Yokoyama S]] |
| - | [[Category: Yokoyama, S]] | + | |
| - | [[Category: Rsgi]]
| + | |
| - | [[Category: Transferase]]
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| Structural highlights
Function
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).
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ishii R, Nureki O, Yokoyama S. Crystal structure of the tRNA processing enzyme RNase PH from Aquifex aeolicus. J Biol Chem. 2003 Aug 22;278(34):32397-404. Epub 2003 May 12. PMID:12746447 doi:http://dx.doi.org/10.1074/jbc.M300639200
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