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3pla

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Crystal structure of a catalytically active substrate-bound box C/D RNP from Sulfolobus solfataricus

Structural highlights

3pla is a 15 chain structure with sequence from Saccharolobus solfataricus, Saccharolobus solfataricus 98/2 and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.15Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

D0KRE2_SACS9 Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, the RNA component of RNase P, box H/ACA, box C/D and box C'/D' sRNAs.[HAMAP-Rule:MF_00326]

Publication Abstract from PubMed

Box C/D RNA protein complexes (RNPs) direct site-specific 2'-O-methylation of RNA and ribosome assembly. The guide RNA in C/D RNP forms base pairs with complementary substrates and selects the modification site using a molecular ruler. Despite many studies of C/D RNP structure, the fundamental questions of how C/D RNAs assemble into RNPs and how they guide modification remain unresolved. Here we report the crystal structure of an entire catalytically active archaeal C/D RNP consisting of a bipartite C/D RNA associated with two substrates and two copies each of Nop5, L7Ae and fibrillarin at 3.15-A resolution. The substrate pairs with the second through the eleventh nucleotide of the 12-nucleotide guide, and the resultant duplex is bracketed in a channel with flexible ends. The methyltransferase fibrillarin binds to an undistorted A-form structure of the guide-substrate duplex and specifically loads the target ribose into the active site. Because interaction with the RNA duplex alone does not determine the site specificity, fibrillarin is further positioned by non-specific and specific protein interactions. Compared with the structure of the inactive C/D RNP, extensive domain movements are induced by substrate loading. Our results reveal the organization of a monomeric C/D RNP and the mechanism underlying its site-specific methylation activity.

Structural basis for site-specific ribose methylation by box C/D RNA protein complexes.,Lin J, Lai S, Jia R, Xu A, Zhang L, Lu J, Ye K Nature. 2011 Jan 27;469(7331):559-563. PMID:21270896^[1]

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

References

↑ Lin J, Lai S, Jia R, Xu A, Zhang L, Lu J, Ye K. Structural basis for site-specific ribose methylation by box C/D RNA protein complexes. Nature. 2011 Jan 27;469(7331):559-563. PMID:21270896 doi:10.1038/nature09688

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==Crystal structure of a catalytically active substrate-bound box C/D RNP from Sulfolobus solfataricus==
-<StructureSection load='3pla' size='340' side='right' caption='[[3pla]], [[Resolution|resolution]] 3.15&Aring;' scene=''>
+<StructureSection load='3pla' size='340' side='right'caption='[[3pla]], [[Resolution|resolution]] 3.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3pla]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/'saccharolobus_solfataricus' 'saccharolobus solfataricus'] and [http://en.wikipedia.org/wiki/Suls9 Suls9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PLA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PLA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3pla]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus], [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_98/2 Saccharolobus solfataricus 98/2] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PLA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PLA FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 3.15&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SSO0939 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 'Saccharolobus solfataricus']), rpl7ae, Ssol_1068 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=555311 SULS9]), flpA, SSO0940, C33_014 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 'Saccharolobus solfataricus'])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></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=3pla FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pla OCA], [http://pdbe.org/3pla PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pla RCSB], [http://www.ebi.ac.uk/pdbsum/3pla PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pla ProSAT]</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=3pla FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pla OCA], [https://pdbe.org/3pla PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pla RCSB], [https://www.ebi.ac.uk/pdbsum/3pla PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pla ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/FLPA_SULSO FLPA_SULSO]] Involved in pre-rRNA and tRNA processing. Utilizes the methyl donor S-adenosyl-L-methionine to catalyze the site-specific 2'-hydroxyl methylation of ribose moieties in rRNA and tRNA. Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA.<ref>PMID:11959980</ref> <ref>PMID:15522081</ref>  [[http://www.uniprot.org/uniprot/D0KRE2_SULS9 D0KRE2_SULS9]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, the RNA component of RNase P, box H/ACA, box C/D and box C'/D' sRNAs.[HAMAP-Rule:MF_00326]
+[https://www.uniprot.org/uniprot/D0KRE2_SACS9 D0KRE2_SACS9] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, the RNA component of RNase P, box H/ACA, box C/D and box C'/D' sRNAs.[HAMAP-Rule:MF_00326]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 *[[Kink-turn motif|Kink-turn motif]]
 *[[Ribosomal protein L7/L12|Ribosomal protein L7/L12]]
-*[[User:Wayne Decatur/NASCE2011|User:Wayne Decatur/NASCE2011]]
-*[[User:Wayne Decatur/UNH CME Workshop March 11 2011|User:Wayne Decatur/UNH CME Workshop March 11 2011]]
-*[[User:Wayne Decatur/UNH Seminar Feb 1st 2011|User:Wayne Decatur/UNH Seminar Feb 1st 2011]]
 *[[User:Wayne Decatur/kink-turn motif|User:Wayne Decatur/kink-turn motif]]
 == References ==
@@ Line 31: / Line 28: @@
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharolobus solfataricus]]
-[[Category: Suls9]]
+[[Category: Saccharolobus solfataricus 98/2]]
-[[Category: Jia, R]]
+[[Category: Synthetic construct]]
-[[Category: Lai, S]]
+[[Category: Jia R]]
-[[Category: Lin, J]]
+[[Category: Lai S]]
-[[Category: Lu, J]]
+[[Category: Lin J]]
-[[Category: Xu, A]]
+[[Category: Lu J]]
-[[Category: Ye, K]]
+[[Category: Xu A]]
-[[Category: Zhang, L]]
+[[Category: Ye K]]
-[[Category: Box c/d rna]]
+[[Category: Zhang L]]
-[[Category: Guide rna]]
-[[Category: Methyltransferase]]
-[[Category: Rna-binding]]
-[[Category: Rna-protein complex]]
-[[Category: Sam]]
-[[Category: Transferase-rna complex]]

3pla

From Proteopedia

Current revision

Crystal structure of a catalytically active substrate-bound box C/D RNP from Sulfolobus solfataricus

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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