This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
2i82
From Proteopedia
(Difference between revisions)
| (12 intermediate revisions not shown.) | |||
| Line 1: | Line 1: | ||
| - | [[Image:2i82.gif|left|200px]] | ||
| - | + | ==Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure== | |
| - | + | <StructureSection load='2i82' size='340' side='right'caption='[[2i82]], [[Resolution|resolution]] 2.05Å' scene=''> | |
| - | + | == Structural highlights == | |
| - | | | + | <table><tr><td colspan='2'>[[2i82]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2I82 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2I82 FirstGlance]. <br> |
| - | | | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FOU:(5S,6R)-5-FLUORO-6-HYDROXYDIHYDROPYRIMIDINE-2,4(1H,3H)-DIONE'>FOU</scene></td></tr> |
| - | + | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=N:ANY+5-MONOPHOSPHATE+NUCLEOTIDE'>N</scene></td></tr> | |
| - | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rluA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | |
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] </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=2i82 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2i82 OCA], [https://pdbe.org/2i82 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2i82 RCSB], [https://www.ebi.ac.uk/pdbsum/2i82 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2i82 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == 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/i8/2i82_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=2i82 ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | RluA is a dual-specificity enzyme responsible for pseudouridylating 23S rRNA and several tRNAs. The 2.05 A resolution structure of RluA bound to a substrate RNA comprising the anticodon stem loop of tRNA(Phe) reveals that enzyme binding induces a dramatic reorganization of the RNA. Instead of adopting its canonical U turn conformation, the anticodon loop folds into a new structure with a reverse-Hoogsteen base pair and three flipped-out nucleotides. Sequence conservation, the cocrystal structure, and the results of structure-guided mutagenesis suggest that RluA recognizes its substrates indirectly by probing RNA loops for their ability to adopt the reorganized fold. The planar, cationic side chain of an arginine intercalates between the reverse-Hoogsteen base pair and the bottom pair of the anticodon stem, flipping the nucleotide to be modified into the active site of RluA. Sequence and structural comparisons suggest that pseudouridine synthases of the RluA, RsuA, and TruA families employ an equivalent arginine for base flipping. | ||
| - | + | Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure.,Hoang C, Chen J, Vizthum CA, Kandel JM, Hamilton CS, Mueller EG, Ferre-D'Amare AR Mol Cell. 2006 Nov 17;24(4):535-45. PMID:17188032<ref>PMID:17188032</ref> | |
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 2i82" style="background-color:#fffaf0;"></div> | ||
| - | == | + | ==See Also== |
| - | + | *[[Guide-independent Pseudouridine synthase|Guide-independent Pseudouridine synthase]] | |
| - | + | *[[Pseudouridine synthase 3D structures|Pseudouridine synthase 3D structures]] | |
| - | + | == References == | |
| - | + | <references/> | |
| - | + | __TOC__ | |
| - | == | + | </StructureSection> |
| - | + | [[Category: Bacillus coli migula 1895]] | |
| - | [[Category: | + | [[Category: Large Structures]] |
[[Category: Pseudouridylate synthase]] | [[Category: Pseudouridylate synthase]] | ||
| - | + | [[Category: Hoang, C]] | |
| - | [[Category: Hoang, C | + | [[Category: Lyase-rna complex]] |
| - | [[Category: | + | [[Category: Pseudouridine synthase]] |
| - | [[Category: | + | |
| - | + | ||
| - | + | ||
Current revision
Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure
| |||||||||||
