Structural organization of box C/D RNA-guided RNA methyltransferase.
Box 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.
Ye
Keqiong
K
National Institute of Biological Sciences, Beijing 102206, China.
Jia
Ru
R
Lin
Jinzhong
J
Ju
Minghua
M
Peng
Jin
J
Xu
Anbi
A
Zhang
Liman
L
D020816:Amino Acid Motifs; D019843:Archaeal Proteins / Q000737:chemistry; D001483:Base Sequence; D002352:Carrier Proteins / Q000737:chemistry*; D002384:Catalysis; D002868:Chromosomal Proteins, Non-Histone / Q000737:chemistry; D018360:Crystallography, X-Ray / Q000379:methods; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D015202:Protein Engineering / Q000379:methods; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry; D019642:RNA, Archaeal / Q000737:chemistry; D012359:tRNA Methyltransferases / Q000737:chemistry*
D019843:Archaeal Proteins; D002352:Carrier Proteins; D002868:Chromosomal Proteins, Non-Histone; D019642:RNA, Archaeal; C047458:fibrillarin; D012313:RNA; D012359:tRNA Methyltransferases