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| | ==Crystal structure of pseudouridine synthase RluD catalytic module== | | ==Crystal structure of pseudouridine synthase RluD catalytic module== |
| - | <StructureSection load='1prz' size='340' side='right' caption='[[1prz]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='1prz' size='340' side='right'caption='[[1prz]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1prz]] is a 1 chain structure with sequence from [http://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=1PRZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PRZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1prz]] 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=1PRZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PRZ FirstGlance]. <br> |
| - | </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></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]] 1.8Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RLUD or SFHB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></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=1prz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1prz OCA], [https://pdbe.org/1prz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1prz RCSB], [https://www.ebi.ac.uk/pdbsum/1prz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1prz ProSAT], [https://www.topsan.org/Proteins/BSGI/1prz 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=1prz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1prz OCA], [http://pdbe.org/1prz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1prz RCSB], [http://www.ebi.ac.uk/pdbsum/1prz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1prz ProSAT], [http://www.topsan.org/Proteins/BSGI/1prz TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RLUD_ECO57 RLUD_ECO57]] Responsible for synthesis of pseudouridine from uracil at positions 1911, 1915 and 1917 in 23S ribosomal RNA (By similarity). | + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pr/1prz_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pr/1prz_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | </div> | | </div> |
| | <div class="pdbe-citations 1prz" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 1prz" 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 == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: Pseudouridylate synthase]] | + | [[Category: Large Structures]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Cygler M]] |
| - | [[Category: Cygler, M]] | + | [[Category: Iannuzzi P]] |
| - | [[Category: Iannuzzi, P]] | + | [[Category: Matte A]] |
| - | [[Category: Matte, A]] | + | [[Category: Sivaraman J]] |
| - | [[Category: Sivaraman, J]] | + | |
| - | [[Category: Bsgi]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Pseudouridine synthase]]
| + | |
| - | [[Category: Rlud]]
| + | |
| Structural highlights
Function
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.[1] [2]
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
Pseudouridine (5-beta-D-ribofuranosyluracil, Psi) is the most commonly found modified base in RNA. Conversion of uridine to Psi is performed enzymatically in both prokaryotes and eukaryotes by pseudouridine synthases (EC 4.2.1.70). The Escherichia coli Psi-synthase RluD modifies uridine to Psi at positions 1911, 1915 and 1917 within 23S rRNA. RluD also possesses a second function related to proper assembly of the 50S ribosomal subunit that is independent of Psi-synthesis. Here, we report the crystal structure of the catalytic module of RluD (residues 68-326; DeltaRluD) refined at 1.8A to a final R-factor of 21.8% (R(free)=24.3%). DeltaRluD is a monomeric enzyme having an overall mixed alpha/beta fold. The DeltaRluD molecule consists of two subdomains, a catalytic subdomain and C-terminal subdomain with the RNA-binding cleft formed by loops extending from the catalytic sub-domain. The catalytic sub-domain of DeltaRluD has a similar fold as in TruA, TruB and RsuA, with the location of the RNA-binding cleft, active-site and conserved, catalytic Asp residue superposing in all four structures. Superposition of the crystal structure of TruB bound to a T-stem loop with RluD reveals that similar RNA-protein interactions for the flipped-out uridine base would exist in both structures, implying that base-flipping is necessary for catalysis. This observation also implies that the specificity determinants for site-specific RNA-binding and recognition likely reside in parts of RluD beyond the active site.
Crystal structure of the RluD pseudouridine synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli.,Sivaraman J, Iannuzzi P, Cygler M, Matte A J Mol Biol. 2004 Jan 2;335(1):87-101. PMID:14659742[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Wrzesinski J, Bakin A, Ofengand J, Lane BG. Isolation and properties of Escherichia coli 23S-RNA pseudouridine 1911, 1915, 1917 synthase (RluD). IUBMB Life. 2000 Jul;50(1):33-7. PMID:11087118 doi:http://dx.doi.org/10.1080/15216540050176566
- ↑ Leppik M, Peil L, Kipper K, Liiv A, Remme J. Substrate specificity of the pseudouridine synthase RluD in Escherichia coli. FEBS J. 2007 Nov;274(21):5759-66. Epub 2007 Oct 12. PMID:17937767 doi:http://dx.doi.org/10.1111/j.1742-4658.2007.06101.x
- ↑ Sivaraman J, Iannuzzi P, Cygler M, Matte A. Crystal structure of the RluD pseudouridine synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli. J Mol Biol. 2004 Jan 2;335(1):87-101. PMID:14659742
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