1v9k

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[[Image:1v9k.gif|left|200px]]
 
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{{Structure
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==The crystal structure of the catalytic domain of pseudouridine synthase RluC from Escherichia coli==
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|PDB= 1v9k |SIZE=350|CAPTION= <scene name='initialview01'>1v9k</scene>, resolution 2.00&Aring;
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<StructureSection load='1v9k' size='340' side='right'caption='[[1v9k]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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<table><tr><td colspan='2'>[[1v9k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V9K FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] </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&#8491;</td></tr>
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|GENE= RLUC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1v9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9k OCA], [https://pdbe.org/1v9k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v9k RCSB], [https://www.ebi.ac.uk/pdbsum/1v9k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9k ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1v9k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9k OCA], [http://www.ebi.ac.uk/pdbsum/1v9k PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1v9k RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/RLUC_ECOLI RLUC_ECOLI] Responsible for synthesis of pseudouridine from uracil at positions 955, 2504 and 2580 in 23S ribosomal RNA.
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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/v9/1v9k_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1v9k 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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The most frequent modification of RNA, the conversion of uridine bases to pseudouridines, is found in all living organisms and often in highly conserved locations in ribosomal and transfer RNA. RluC and RluD are homologous enzymes which each convert three specific uridine bases in Escherichia coli ribosomal 23S RNA to pseudouridine: bases 955, 2504, and 2580 in the case of RluC and 1911, 1915, and 1917 in the case of RluD. Both have an N-terminal S4 RNA binding domain. While the loss of RluC has little phenotypic effect, loss of RluD results in a much reduced growth rate. We have determined the crystal structures of the catalytic domain of RluC, and full-length RluD. The S4 domain of RluD appears to be highly flexible or unfolded and is completely invisible in the electron density map. Despite the conserved topology shared by the two proteins, the surface shape and charge distribution are very different. The models suggest significant differences in substrate binding by different pseudouridine synthases.
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'''The crystal structure of the catalytic domain of pseudouridine synthase RluC from Escherichia coli'''
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Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli.,Mizutani K, Machida Y, Unzai S, Park SY, Tame JR Biochemistry. 2004 Apr 20;43(15):4454-63. PMID:15078091<ref>PMID:15078091</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 1v9k" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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The most frequent modification of RNA, the conversion of uridine bases to pseudouridines, is found in all living organisms and often in highly conserved locations in ribosomal and transfer RNA. RluC and RluD are homologous enzymes which each convert three specific uridine bases in Escherichia coli ribosomal 23S RNA to pseudouridine: bases 955, 2504, and 2580 in the case of RluC and 1911, 1915, and 1917 in the case of RluD. Both have an N-terminal S4 RNA binding domain. While the loss of RluC has little phenotypic effect, loss of RluD results in a much reduced growth rate. We have determined the crystal structures of the catalytic domain of RluC, and full-length RluD. The S4 domain of RluD appears to be highly flexible or unfolded and is completely invisible in the electron density map. Despite the conserved topology shared by the two proteins, the surface shape and charge distribution are very different. The models suggest significant differences in substrate binding by different pseudouridine synthases.
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*[[Guide-independent Pseudouridine synthase|Guide-independent Pseudouridine synthase]]
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*[[Pseudouridine synthase 3D structures|Pseudouridine synthase 3D structures]]
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==About this Structure==
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== References ==
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1V9K is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V9K OCA].
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<references/>
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__TOC__
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==Reference==
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</StructureSection>
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Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli., Mizutani K, Machida Y, Unzai S, Park SY, Tame JR, Biochemistry. 2004 Apr 20;43(15):4454-63. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15078091 15078091]
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[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Pseudouridylate synthase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Machida Y]]
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[[Category: Machida, Y.]]
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[[Category: Mizutani K]]
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[[Category: Mizutani, K.]]
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[[Category: Park S-Y]]
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[[Category: Park, S Y.]]
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[[Category: Tame JRH]]
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[[Category: Tame, J R.H.]]
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[[Category: Unzai S]]
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[[Category: Unzai, S.]]
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[[Category: pseudouridine syntase]]
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[[Category: rna binding]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:21:20 2008''
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Current revision

The crystal structure of the catalytic domain of pseudouridine synthase RluC from Escherichia coli

PDB ID 1v9k

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