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5gin

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Revision as of 06:44, 13 May 2020

Crystal structure of box C/D RNP with 12 nt guide regions and 9 nt substrates

Structural highlights

5gin is a 15 chain structure with sequence from Atcc 35091. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	5gip, 5gio
Gene:	SULA_1947, SULB_1948, SULC_1946 (ATCC 35091), rpl7ae, SULA_1106, SULB_1107, SULC_1105 (ATCC 35091), flpA, SSOP1_0970, SULA_1948, SULB_1949, SULC_1947 (ATCC 35091)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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] [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]

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

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5gin"

@@ Line 1: / Line 1: @@
 ==Crystal structure of box C/D RNP with 12 nt guide regions and 9 nt substrates==
-<StructureSection load='5gin' size='340' side='right' caption='[[5gin]], [[Resolution|resolution]] 3.31&Aring;' scene=''>
+<StructureSection load='5gin' size='340' side='right'caption='[[5gin]], [[Resolution|resolution]] 3.31&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5gin]] is a 15 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GIN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GIN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5gin]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35091 Atcc 35091]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GIN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GIN 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='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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5gip|5gip]], [[5gio|5gio]]</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=5gin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gin OCA], [http://pdbe.org/5gin PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gin RCSB], [http://www.ebi.ac.uk/pdbsum/5gin PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gin ProSAT]</span></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SULA_1947, SULB_1948, SULC_1946 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091]), rpl7ae, SULA_1106, SULB_1107, SULC_1105 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 ATCC 35091]), flpA, SSOP1_0970, SULA_1948, SULB_1949, SULC_1947 ([http://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'>[http://proteopedia.org/fgij/fg.htm?mol=5gin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gin OCA], [http://pdbe.org/5gin PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gin RCSB], [http://www.ebi.ac.uk/pdbsum/5gin PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gin ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 23: / Line 24: @@
 __TOC__
 </StructureSection>
+[[Category: Atcc 35091]]
+[[Category: Large Structures]]
 [[Category: Lin, J]]
 [[Category: Yang, Z]]

5gin

From Proteopedia

Revision as of 06:44, 13 May 2020

Crystal structure of box C/D RNP with 12 nt guide regions and 9 nt substrates

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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