3lwp

From Proteopedia

(Difference between revisions)

Revision as of 19:41, 5 August 2016

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

Structural highlights

3lwp is a 5 chain structure with sequence from Atcc 43587. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:	3lwo, 3lwq, 3lwr, 3lwv
Gene:	truB, PF1785 (ATCC 43587), PF1141 (ATCC 43587), PF1367, rpl7ae (ATCC 43587)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[TRUB_PYRFU] Could be responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs (By similarity). [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). [NOP10_PYRFU] Involved in ribosome biogenesis; more specifically in 18S rRNA pseudouridylation and in cleavage of pre-rRNA (By similarity).

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

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Zhou J, Lv C, Liang B, Chen M, Yang W, Li H. Glycosidic bond conformation preference plays a pivotal role in catalysis of RNA pseudouridylation: a combined simulation and structural study. J Mol Biol. 2010 Sep 3;401(5):690-5. Epub 2010 Jul 6. PMID:20615421 doi:10.1016/j.jmb.2010.06.061

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3lwp"

@@ Line 1: / Line 1: @@
 ==Structure of H/ACA RNP bound to a substrate RNA containing 5BrdU==
 <StructureSection load='3lwp' size='340' side='right' caption='[[3lwp]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3lwp]] is a 5 chain structure 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LWP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3lwp]] 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=3LWP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LWP FirstGlance]. <br>
 </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=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3lwo|3lwo]], [[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 Pyrococcus furiosus]), PF1141 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus]), PF1367, rpl7ae ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus])</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=3lwp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lwp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lwp RCSB], [http://www.ebi.ac.uk/pdbsum/3lwp PDBsum]</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=3lwp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lwp OCA], [http://pdbe.org/3lwp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lwp RCSB], [http://www.ebi.ac.uk/pdbsum/3lwp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lwp ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 20: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 29: / Line 30: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3lwp" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 36: / Line 38: @@
 __TOC__
 </StructureSection>
-[[Category: Pyrococcus furiosus]]
+[[Category: Atcc 43587]]
 [[Category: Li, H]]
 [[Category: Liang, B]]

3lwp

From Proteopedia

Revision as of 19:41, 5 August 2016

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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