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.


3lwo

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:00, 9 January 2019) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:3lwo.png|left|200px]]
 
-
<!--
+
==Structure of H/ACA RNP bound to a substrate RNA containing 5BrU==
-
The line below this paragraph, containing "STRUCTURE_3lwo", creates the "Structure Box" on the page.
+
<StructureSection load='3lwo' size='340' side='right' caption='[[3lwo]], [[Resolution|resolution]] 2.85&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'>[[3lwo]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LWO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LWO FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
-->
+
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene></td></tr>
-
{{STRUCTURE_3lwo| PDB=3lwo | SCENE= }}
+
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3lwp|3lwp]], [[3lwq|3lwq]], [[3lwr|3lwr]], [[3lwv|3lwv]]</td></tr>
 +
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">truB, PF1785 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587]), PF1141 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587]), PF1367, rpl7ae ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</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=3lwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lwo OCA], [http://pdbe.org/3lwo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lwo RCSB], [http://www.ebi.ac.uk/pdbsum/3lwo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lwo ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[[http://www.uniprot.org/uniprot/TRUB_PYRFU TRUB_PYRFU]] Could be responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs (By similarity). [[http://www.uniprot.org/uniprot/RL7A_PYRFU RL7A_PYRFU]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs (By similarity). [[http://www.uniprot.org/uniprot/NOP10_PYRFU NOP10_PYRFU]] Involved in ribosome biogenesis; more specifically in 18S rRNA pseudouridylation and in cleavage of pre-rRNA (By similarity).
 +
== 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/lw/3lwo_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=3lwo ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
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.
-
===Structure of H/ACA RNP bound to a substrate RNA containing 5BrU===
+
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>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 3lwo" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_20615421}}, 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 20615421 is the PubMed ID number.
+
*[[Ribosome biogenesis protein|Ribosome biogenesis protein]]
-
-->
+
== References ==
-
{{ABSTRACT_PUBMED_20615421}}
+
<references/>
-
 
+
__TOC__
-
==About this Structure==
+
</StructureSection>
-
3LWO is a 5 chains structure with sequences 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=3LWO OCA].
+
[[Category: Atcc 43587]]
-
 
+
[[Category: Li, H]]
-
==Reference==
+
[[Category: Liang, B]]
-
<ref group="xtra">PMID:20615421</ref><references group="xtra"/>
+
[[Category: Lv, C]]
-
[[Category: Pyrococcus furiosus]]
+
[[Category: Yang, W]]
-
[[Category: Li, H.]]
+
[[Category: Zhou, J]]
-
[[Category: Liang, B.]]
+
-
[[Category: Lv, C.]]
+
-
[[Category: Yang, W.]]
+
-
[[Category: Zhou, J.]]
+
[[Category: H/aca pseudouridine synthase]]
[[Category: H/aca pseudouridine synthase]]
[[Category: Isomerase]]
[[Category: Isomerase]]
Line 39: Line 54:
[[Category: Rrna processing]]
[[Category: Rrna processing]]
[[Category: Trna processing]]
[[Category: Trna processing]]
- 
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 1 09:18:49 2010''
 

Current revision

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

3lwo, resolution 2.85Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3lwo"
Personal tools