3id5: Difference between revisions
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==Crystal structure of Sulfolobus solfataricus C/D RNP assembled with Nop5, fibrillarin, L7Ae and a split half C/D RNA== | ==Crystal structure of Sulfolobus solfataricus C/D RNP assembled with Nop5, fibrillarin, L7Ae and a split half C/D RNA== | ||
<StructureSection load='3id5' size='340' side='right' caption='[[3id5]], [[Resolution|resolution]] 4.01Å' scene=''> | <StructureSection load='3id5' size='340' side='right'caption='[[3id5]], [[Resolution|resolution]] 4.01Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3id5]] is a 8 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3id5]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_35091 Atcc 35091]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ID5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ID5 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3id6|3id6]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3id6|3id6]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SSO0939 ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SSO0939 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091]), flpA, SSO0940, C33_014 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091]), rpl7ae, SSO0091, C04_031 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091])</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3id5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3id5 OCA], [https://pdbe.org/3id5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3id5 RCSB], [https://www.ebi.ac.uk/pdbsum/3id5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3id5 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[ | [[https://www.uniprot.org/uniprot/RL7A_SULSO RL7A_SULSO]] 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/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> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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==See Also== | ==See Also== | ||
*[[Aldehyde dehydrogenase|Aldehyde dehydrogenase]] | *[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Atcc 35091]] | [[Category: Atcc 35091]] | ||
[[Category: Large Structures]] | |||
[[Category: Ye, K]] | [[Category: Ye, K]] | ||
[[Category: 2'-o-methylation]] | [[Category: 2'-o-methylation]] | ||
Revision as of 10:46, 10 November 2021
Crystal structure of Sulfolobus solfataricus C/D RNP assembled with Nop5, fibrillarin, L7Ae and a split half C/D RNACrystal structure of Sulfolobus solfataricus C/D RNP assembled with Nop5, fibrillarin, L7Ae and a split half C/D RNA
Structural highlights
Function[RL7A_SULSO] 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). [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.[1] [2] 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 PubMedBox C/D guide RNAs are abundant noncoding RNAs that primarily function to direct the 2'-O-methylation of specific nucleotides by base-pairing with substrate RNAs. In archaea, a bipartite C/D RNA assembles with L7Ae, Nop5, and the methyltransferase fibrillarin into a modification enzyme with unique substrate specificity. Here, we determined the crystal structure of an archaeal C/D RNA-protein complex (RNP) composed of all 3 core proteins and an engineered half-guide RNA at 4 A resolution, as well as 2 protein substructures at higher resolution. The RNP structure reveals that the C-terminal domains of Nop5 in the dimeric complex provide symmetric anchoring sites for 2 L7Ae-associated kink-turn motifs of the C/D RNA. A prominent protrusion in Nop5 seems to be important for guide RNA organization and function and for discriminating the structurally related U4 snRNA. Multiple conformations of the N-terminal domain of Nop5 and its associated fibrillarin in different structures indicate the inherent flexibility of the catalytic module, suggesting that a swinging motion of the catalytic module is part of the enzyme mechanism. We also built a model of a native C/D RNP with substrate and fibrillarin in an active conformation. Our results provide insight into the overall organization and mechanism of action of C/D RNA-guided RNA methyltransferases. Structural organization of box C/D RNA-guided RNA methyltransferase.,Ye K, Jia R, Lin J, Ju M, Peng J, Xu A, Zhang L Proc Natl Acad Sci U S A. 2009 Aug 5. PMID:19666563[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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