5gip | pdb_00005gip
Crystal structure of box C/D RNP with 13 nt guide regions and 11 nt substrates
Structural highlights
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 PubMedBox 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
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