3lwp

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[[Image:3lwp.png|left|200px]]
 
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==Structure of H/ACA RNP bound to a substrate RNA containing 5BrdU==
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The line below this paragraph, containing "STRUCTURE_3lwp", creates the "Structure Box" on the page.
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<StructureSection load='3lwp' size='340' side='right'caption='[[3lwp]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3lwp]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LWP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LWP FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.5&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_3lwp| PDB=3lwp | SCENE= }}
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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=3lwp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lwp OCA], [https://pdbe.org/3lwp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lwp RCSB], [https://www.ebi.ac.uk/pdbsum/3lwp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lwp ProSAT]</span></td></tr>
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</table>
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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/lw/3lwp_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=3lwp 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 abundant chemical modification on RNA is isomerization of uridine (or pseudouridylation) catalyzed by pseudouridine synthases. The catalytic mechanism of this essential process remains largely speculative, partly due to lack of knowledge of the pre-reactive state that is important to the identification of reactive chemical moieties. In the present study, we showed, using orthogonal space random-walk free-energy simulation, that the pre-reactive states of uridine and its reactive derivative 5-fluorouridine, bound to a ribonucleoprotein particle pseudouridine synthase, strongly prefer the syn glycosidic bond conformation, while that of the nonreactive 5-bromouridine-containing substrate is largely populated in the anti conformation state. A high-resolution crystal structure of the 5-bromouridine-containing substrate bound to the ribonucleoprotein particle pseudouridine synthase and enzyme activity assay confirmed the anti nonreactive conformation and provided the molecular basis for its confinement. The observed preference for the syn pre-reactive state by the enzyme-bound uridine may help to distinguish among currently proposed mechanisms.
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===Structure of H/ACA RNP bound to a substrate RNA containing 5BrdU===
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Glycosidic bond conformation preference plays a pivotal role in catalysis of RNA pseudouridylation: a combined simulation and structural study.,Zhou J, Lv C, Liang B, Chen M, Yang W, Li H J Mol Biol. 2010 Sep 3;401(5):690-5. Epub 2010 Jul 6. PMID:20615421<ref>PMID:20615421</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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The line below this paragraph, {{ABSTRACT_PUBMED_20615421}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3lwp" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 20615421 is the PubMed ID number.
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{{ABSTRACT_PUBMED_20615421}}
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==About this Structure==
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[[3lwp]] is a 5 chain structure of [[Ribosomal protein L7]] with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LWP OCA].
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==See Also==
==See Also==
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*[[Ribosomal protein L7]]
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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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==Reference==
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*[[Ribosome biogenesis protein 3D structures|Ribosome biogenesis protein 3D structures]]
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<ref group="xtra">PMID:20615421</ref><references group="xtra"/>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pyrococcus furiosus]]
[[Category: Pyrococcus furiosus]]
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[[Category: Li, H.]]
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[[Category: Li H]]
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[[Category: Liang, B.]]
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[[Category: Liang B]]
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[[Category: Lv, C.]]
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[[Category: Lv C]]
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[[Category: Yang, W.]]
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[[Category: Yang W]]
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[[Category: Zhou, J.]]
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[[Category: Zhou J]]
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[[Category: H/aca pseudouridine synthase]]
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[[Category: Isomerase]]
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[[Category: Isomerase-rna binding protein-rna complex]]
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[[Category: Ribonucleoprotein]]
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[[Category: Ribosomal protein]]
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[[Category: Ribosome biogenesis]]
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[[Category: Rna-binding]]
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[[Category: Rrna processing]]
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[[Category: Trna processing]]
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Current revision

Structure of H/ACA RNP bound to a substrate RNA containing 5BrdU

PDB ID 3lwp

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