Modomics - A Database of RNA Modifications

ID Card:

Full name: rRNA 2′-O-methyltransferase fibrillarin
Synonym: Fibrillarin, Lot3p
GI: 6320190
Orf: YDL014W
COG: COG1889
UniProt: P15646
Alpha Fold Predicted Structure: AF-P15646-F1
Complex: C/D RNP
Enzyme type: methyltransferase
Position of modification - modification: s:many - Xm
l:many - Xm



Protein sequence:

MSFRPGSRGGSRGGSRGGFGGRGGSRGGARGGSRGGFGGRGGSRGGARGGSRGGFGGRGGSRGGARGGSRGGRGGAAGGARGGAKVVIEPHRHAGVYIARGKEDLLVTKNMAPGESVYGEKRISVEEPSKEDGVPPTKVEYRVWNPFRSKLAAGIMGGLDELFIAPGKKVLYLGAASGTSVSHVSDVVGPEGVVYAVEFSHRPGRELISMAKKRPNIIPIIEDARHPQKYRMLIGMVDCVFADVAQPDQARIIALNSHMFLKDQGGVVISIKANCIDSTVDAETVFAREVQKLREERIKPLEQLTLEPYERDHCIVVGRYMRSGLKK

Comments:

This is a methyltransferase that depends on S-adenosyl-L-methionine, capable of methylating both RNA and proteins. It plays a role in pre-rRNA processing by performing site-specific 2'-hydroxyl methylation on ribose moieties in pre-ribosomal RNA ( Schimmang et al. 1989, Tollervey et al. 1991, Galardi et al. 2002). The specificity of the methylation site is determined by a guide RNA that pairs with the substrate, with the methylation occurring at a characteristic distance from the sequence involved in base pairing ( Schimmang et al. 1989, Tollervey et al. 1991). This enzyme is also involved in the biogenesis of 18S rRNA. Furthermore, it functions as a protein methyltransferase, catalyzing the methylation of histone H2A's 'Gln-105' (H2AQ105me). This modification impairs binding of the FACT complex and is specifically present at the 35S ribosomal DNA locus ( Schimmang et al. 1989, Tollervey et al. 1991). It is the catalytic subunit of a multiprotein C/D RNP complex. Works in S. cerevisiae with 3 other proteins: Nop58p, Nop56p, Snu13p. About 53 positions methylated by C/D RNP complex were found in S. cerevisiae rRNA




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
A:Am RNA rRNA many Nucleolus
G:Gm RNA rRNA many Nucleolus
C:Cm RNA rRNA many Nucleolus
U:Um RNA rRNA many Nucleolus
N:Nm undefined RNA ()   3'end

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P15646-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P15646-F1.cif  
DSSP Secondary Structures   P15646.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Isolation and sequencing of NOP1. A yeast gene encoding a nucleolar protein homologous to a human autoimmune antigen. Henriquez R, Blobel G, Aris JP J Biol Chem [details] 2298745 -
Nucleolar KKE/D repeat proteins Nop56p and Nop58p interact with Nop1p and are required for ribosome biogenesis. Gautier T, Berges T, Tollervey D, Hurt E Mol Cell Biol [details] 9372940 -
The small nucleolar RNP protein NOP1 (fibrillarin) is required for pre-rRNA processing in yeast. Tollervey D, Lehtonen H, Carmo-Fonseca M, Hurt EC EMBO J [details] 1825809 -
A U3 snoRNP protein with homology to splicing factor PRP4 and G beta domains is required for ribosomal RNA processing. Jansen R, Tollervey D, Hurt EC EMBO J [details] 8508778 -
Box C/D snoRNP catalysed methylation is aided by additional pre-rRNA base-pairing. van Nues RW, Granneman S, Kudla G, Sloan KE, Chicken M, Tollervey D, Watkins NJ EMBO J [details] 21556049 -

Links:

_Wikipedia_
_SGD_
_The yeast snoRNA database_
_PubMed_