3hax

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of a substrate-bound Gar1-minus H/ACA RNP from Pyrococcus furiosus

Structural highlights

3hax is a 5 chain structure with sequence from Pyrococcus furiosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.11Å
Ligands:	, , , , ,
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).

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

H/ACA RNAs form ribonucleoprotein complex (RNP) with proteins Cbf5, Nop10, L7Ae, and Gar1 and guide site-specific conversion of uridine into pseudouridine in cellular RNAs. The crystal structures of H/ACA RNP with substrate bound at the active site cleft reveal that the substrate is recruited through sequence-specific pairing with guide RNA and essential protein contacts. Substrate binding leads to a reorganization of a preset pseudouridylation pocket and an adaptive movement of the PUA domain and the lower stem of the H/ACA RNA. Moreover, a thumb loop flips from the Gar1-bound state in the substrate-free RNP structure to tightly associate with the substrate. Mutagenesis and enzyme kinetics analysis suggest a critical role of Gar1 and the thumb in substrate turnover, particularly in product release. Comparison with tRNA Psi55 synthase TruB reveals the structural conservation and adaptation between an RNA-guided and stand-alone pseudouridine synthase and provides insight into the guide-independent activity of Cbf5.

Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase.,Duan J, Li L, Lu J, Wang W, Ye K Mol Cell. 2009 May 14;34(4):427-39. PMID:19481523^[1]

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

References

↑ Duan J, Li L, Lu J, Wang W, Ye K. Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase. Mol Cell. 2009 May 14;34(4):427-39. PMID:19481523 doi:10.1016/j.molcel.2009.05.005

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/3hax"

Categories: Large Structures | Pyrococcus furiosus | Ye K

@@ Line 3: / Line 3: @@
 <StructureSection load='3hax' size='340' side='right'caption='[[3hax]], [[Resolution|resolution]] 2.11&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3hax]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HAX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HAX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3hax]] 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=3HAX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HAX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.11&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FHU:(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5-MONOPHOSPHATE'>FHU</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FHU:(5S,6R)-5-FLUORO-6-HYDROXY-PSEUDOURIDINE-5-MONOPHOSPHATE'>FHU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3hay|3hay]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">truB, PF1785 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587]), PF1141 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587]), rpl7ae, PF1367 ([https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3hax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hax OCA], [https://pdbe.org/3hax PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hax RCSB], [https://www.ebi.ac.uk/pdbsum/3hax PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hax ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://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). [[https://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). [[https://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).
+[https://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).
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 36: / Line 34: @@
 *[[Kink-turn motif|Kink-turn motif]]
 *[[Pseudouridine synthase 3D structures|Pseudouridine synthase 3D structures]]
-*[[Ribosome biogenesis protein|Ribosome biogenesis protein]]
+*[[Ribosome biogenesis protein 3D structures|Ribosome biogenesis protein 3D structures]]
 *[[User:Wayne Decatur/kink-turn motif|User:Wayne Decatur/kink-turn motif]]
 == References ==
@@ Line 42: / Line 40: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 43587]]
 [[Category: Large Structures]]
-[[Category: Ye, K]]
+[[Category: Pyrococcus furiosus]]
-[[Category: Guide rna]]
+[[Category: Ye K]]
-[[Category: H/aca]]
-[[Category: Isomerase]]
-[[Category: Isomerase-biosynthetic protein-rna complex]]
-[[Category: Pseudouridine synthase]]
-[[Category: Ribonucleoprotein]]
-[[Category: Ribosomal protein]]
-[[Category: Ribosome biogenesis]]
-[[Category: Rna-binding]]
-[[Category: Rna-protein complex]]
-[[Category: Rrna processing]]
-[[Category: Trna processing]]

3hax

From Proteopedia

Current revision

Crystal structure of a substrate-bound Gar1-minus H/ACA RNP from Pyrococcus furiosus

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox