Modomics - A Database of RNA Modifications

ID Card:

Full name: Fibrillarin-like rRNA/tRNA 2′-O-methyltransferase
Synonym: aFib, Fibrillarin-like
GI: 15897821
Orf: C33_014
COG: COG1889
UniProt: P58032
Structures: | 3PLA | 3ID5 | 3ID6 |
Alpha Fold Predicted Structure: AF-P58032-F1
Complex: C/D RNP
Enzyme type: methyltransferase
Position of modification - modification: l:many - Xm
s:many - Xm


PDB Structures:


3PLA

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

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.

Download RCSB-PDB Structures:

Pdb Files   3ID5.pdb   3ID6.pdb   3PLA.pdb  
Pdbx/mmCIF Files   3ID5.cif   3ID6.cif   3PLA.cif  


Protein sequence:

MSEVITVKQTNMENIYECEFNDGSFRLCTRNLVPNFNVYGERLIKYEGVEYREWNAFRSKLAGAILKGLKTNPIRKGTKVLYLGAASGTTISHVSDIIELNGKAYGVEFSPRVVRELLLVAQRRPNIFPLLADARFPQSYKSVVENVDVLYVDIAQPDQTDIAIYNAKFFLKVNGDMLLVIKARSIDVTKDPKEIYKTEVEKLENSNFETIQIINLDPYDKDHAIVLSKYKG

Comments:

Homologue of yeast Nop1 protein and human fibrillarin. A catalytic subunit of C/D RNP complex, which in Archaea is composed of FlpA (fibrillarin), L7Ae and Nop56/58 proteins.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
N:Nm undefined RNA ()   3'end

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M S E V I T V K Q T N M E N I Y E C E F N D G S F R L C T R N L V P N F N V Y G E R L I K Y E G V E Y R E W N A F R S K L A G A I L K G L K T N P I R K G T K V L Y L G A A S G T T I S H V S D I I E L N G K A Y G V E F S P R V V R E L L L V A Q R R P N I F P L L A D A R F P Q S Y K S V V E N V D V L Y V D I A Q P D Q T D I A I Y N A K F F L K V N G D M L L V I K A R S I D V T K D P K E I Y K T E V E K L E N S N F E T I Q I I N L D P Y D K D H A I V L S K Y K G

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-P58032-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P58032-F1.cif  
DSSP Secondary Structures   P58032.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
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 [details] 19666563 -
Structural basis for site-specific ribose methylation by box C/D RNA protein complexes. Lin J, Lai S, Jia R, Xu A, Zhang L, Lu J, Ye K Nature [details] 21270896 -

Links:

_Wikipedia_
_PubMed_