1v9f: Difference between revisions

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-{{Seed}}
-[[Image:1v9f.png|left|200px]]
-<!--
+==Crystal structure of catalytic domain of pseudouridine synthase RluD from Escherichia coli==
-The line below this paragraph, containing "STRUCTURE_1v9f", creates the "Structure Box" on the page.
+<StructureSection load='1v9f' size='340' side='right'caption='[[1v9f]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1v9f]] is a 1 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=1V9F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V9F FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</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></td></tr>
-{{STRUCTURE_1v9f|  PDB=1v9f  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1v9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v9f OCA], [https://pdbe.org/1v9f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v9f RCSB], [https://www.ebi.ac.uk/pdbsum/1v9f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v9f ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RLUD_ECOLI RLUD_ECOLI] Responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA. Isomerization occurs as a late step during the assembly of the large ribosomal subunit.<ref>PMID:11087118</ref> <ref>PMID:17937767</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v9/1v9f_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1v9f ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-===Crystal structure of catalytic domain of pseudouridine synthase RluD from Escherichia coli===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1v9f" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15078091}}, adds the Publication Abstract to the page
+*[[Guide-independent Pseudouridine synthase|Guide-independent Pseudouridine synthase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15078091 is the PubMed ID number.
+*[[Pseudouridine synthase 3D structures|Pseudouridine synthase 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_15078091}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-V9F 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=1V9F OCA].
-==Reference==
-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]
 [[Category: Escherichia coli]]
-[[Category: Pseudouridylate synthase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Machida Y]]
-[[Category: Machida, Y.]]
+[[Category: Mizutani K]]
-[[Category: Mizutani, K.]]
+[[Category: Park S-Y]]
-[[Category: Park, S Y.]]
+[[Category: Tame JRH]]
-[[Category: Tame, J R.H.]]
+[[Category: Unzai S]]
-[[Category: Unzai, S.]]
-[[Category: Pseudouridine synthase]]
-[[Category: Rna binding]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 02:35:54 2008''