Modomics - A Database of RNA Modifications

ID Card:

Full name: Fibrillarin-like rRNA/tRNA 2′-O-methyltransferase
Synonym: aFib, Fibrillarin-like, AF_2087
GI: 11499669
COG: COG1889
UniProt: O28192
Structures: | 1NT2 |
Alpha Fold Predicted Structure: AF-O28192-F1
Complex: C/D RNP
Enzyme type: methyltransferase
Position of modification - modification: l:many - Xm
s:many - Xm


PDB Structures:


1NT2

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Nop56p and Nop58p are two core proteins of the box C/D snoRNPs that interact concurrently with fibrillarin and snoRNAs to function in enzyme assembly and catalysis. Here we report the 2.9 A resolution co-crystal structure of an archaeal homolog of Nop56p/Nop58p, Nop5p, in complex with fibrillarin from Archaeoglobus fulgidus (AF) and the methyl donor S-adenosyl-L-methionine. The N-terminal domain of Nop5p forms a complementary surface to fibrillarin that serves to anchor the catalytic subunit and to stabilize cofactor binding. A coiled coil in Nop5p mediates dimerization of two fibrillarin-Nop5p heterodimers for optimal interactions with bipartite box C/D RNAs. Structural analysis and complementary biochemical data demonstrate that the conserved C-terminal domain of Nop5p harbors RNA-binding sites. A model of box C/D snoRNP assembly is proposed based on the presented structural and biochemical data.

Download RCSB-PDB Structures:

Pdb Files   1NT2.pdb  
Pdbx/mmCIF Files   1NT2.cif  


Protein sequence:

MKELMRNVYLLDDTLVTKSKYGSHYGEKVFDGYREWVPWRSKLAAMILKGHRLKLRGDERVLYLGAASGTTVSHLADIVDEGIIYAVEYSAKPFEKLLELVRERNNIIPLLFDASKPWKYSGIVEKVDLIYQDIAQKNQIEILKANAEFFLKEKGEVVIMVKARSIDSTAEPEEVFKSVLKEMEGDFKIVKHGSLMPYHRDHIFIHAYRF

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

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-O28192-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-O28192-F1.cif  
DSSP Secondary Structures   O28192.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Structural and thermodynamic evidence for a stabilizing role of Nop5p in S-adenosyl-L-methionine binding to fibrillarin. Aittaleb M, Visone T, Fenley MO, Li H J Biol Chem [details] 15286083 -
Structure and function of archaeal box C/D sRNP core proteins. Aittaleb M, Rashid R, Chen Q, Palmer JR, Daniels CJ, Li H Nat Struct Biol [details] 12598892 -

Links:

_PubMed_