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| | ==Crystal structure of box C/D RNP with 13 nt guide regions and 11 nt substrates== | | ==Crystal structure of box C/D RNP with 13 nt guide regions and 11 nt substrates== |
| - | <StructureSection load='5gip' size='340' side='right' caption='[[5gip]], [[Resolution|resolution]] 3.13Å' scene=''> | + | <StructureSection load='5gip' size='340' side='right'caption='[[5gip]], [[Resolution|resolution]] 3.13Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5gip]] is a 20 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GIP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GIP FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5gip]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GIP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GIP 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]] 3.129Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5gin|5gin]], [[5gio|5gio]]</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=5gip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gip OCA], [http://pdbe.org/5gip PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gip RCSB], [http://www.ebi.ac.uk/pdbsum/5gip PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gip 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=5gip FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gip OCA], [https://pdbe.org/5gip PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gip RCSB], [https://www.ebi.ac.uk/pdbsum/5gip PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gip ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A0A0E3JUC9_SULSF A0A0E3JUC9_SULSF]] 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.[HAMAP-Rule:MF_00351] [[http://www.uniprot.org/uniprot/A0A0E3JZF7_SULSF A0A0E3JZF7_SULSF]] 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/Q97ZH3_SACS2 Q97ZH3_SACS2] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Lin, J]] | + | [[Category: Large Structures]] |
| - | [[Category: Yang, Z]] | + | [[Category: Saccharolobus solfataricus]] |
| - | [[Category: Ye, K]] | + | [[Category: Lin J]] |
| - | [[Category: 2'-o-methylation]] | + | [[Category: Yang Z]] |
| - | [[Category: Guide rna]] | + | [[Category: Ye K]] |
| - | [[Category: Rnp]]
| + | |
| - | [[Category: Transferase-rna complex]]
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| Structural highlights
Function
Q97ZH3_SACS2
Publication Abstract from PubMed
Box C/D RNAs guide site-specific 2'-O-methylation of RNAs in archaea and eukaryotes. The spacer regions between boxes C to D' and boxes C' to D contain the guide sequence that can form a stretch of base pairs with substrate RNAs. The lengths of spacer regions and guide-substrate duplexes are variable among C/D RNAs. In a previously determined structure of C/D ribonucleoprotein (RNP), a 12-nt-long spacer forms 10 bp with the substrate. How spacers and guide-substrate duplexes of other lengths are accommodated remains unknown. Here we analyze how the lengths of spacers and guide-substrate duplexes affect the modification activity and determine three structures of C/D RNPs assembled with different spacers and substrates. We show that the guide can only form a duplex of a maximum of 10 bp with the substrate during modification. Slightly shorter duplexes are tolerated, but longer duplexes must be unwound to fit into a capped protein channel for modification. Spacers with <12 nucleotides are defective, mainly because they cannot load the substrate in the active conformation. For spacers with >12 nucleotides, the excessive unpaired sequences near the box C/C' side are looped out. Our results provide insight into the substrate recognition mechanism of C/D RNA and refute the RNA-swapped model for dimeric C/D RNP.
Box C/D guide RNAs recognize a maximum of 10 nt of substrates.,Yang Z, Lin J, Ye K Proc Natl Acad Sci U S A. 2016 Sep 27;113(39):10878-83. doi:, 10.1073/pnas.1604872113. Epub 2016 Sep 13. PMID:27625427[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yang Z, Lin J, Ye K. Box C/D guide RNAs recognize a maximum of 10 nt of substrates. Proc Natl Acad Sci U S A. 2016 Sep 27;113(39):10878-83. doi:, 10.1073/pnas.1604872113. Epub 2016 Sep 13. PMID:27625427 doi:http://dx.doi.org/10.1073/pnas.1604872113
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