Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal RNA large subunit methyltransferase F
Synonym: YbiN, JW5107
GI: 3915947
Orf: b0807
COG: COG3129
UniProt: P75782
Alpha Fold Predicted Structure: AF-P75782-F1
Enzyme type: methyltransferase
Position of modification - modification: l:1618(1618) - m6A



Protein sequence:

MSAQKPGLHPRNRHHSRYDLATLCQVNPELRQFLTLTPAGEQSVDFANPLAVKALNKALLAHFYAVANWDIPDGFLCPPVPGRADYIHHLADLLAEASGTIPANASILDIGVGANCIYPLIGVHEYGWRFTGSETSSQALSSAQAIISSNPGLNRAIRLRRQKESGAIFNGIIHKNEQYDATLCNPPFHDSAAAARAGSERKRRNLGLNKDDALNFGGQQQELWCEGGEVTFIKKMIEESKGFAKQVMWFTSLVSRGENLPPLYRALTDVGAVKVVKKEMAQGQKQSRFIAWTFMNDEQRRRFVNRQR

Comments:

This enzyme catalyzes the site-specific formation of m6A at position 1618 in the loop of the mini hairpin 59a in domain III of the large subunit of rRNA, located nearby the peptide tunnel of the ribosome. Recombinant RlmF protein is able to methylate partially deproteinized 50S ribosomal subunit, but neither the completely assembled 50S subunits nor completely deproteinized 23S rRNA. AdoMet is the methyl group donor. The C-terminal domain of RlmF is related to the ones of RsmC (m2G1209)/RsmD(m2G966).




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
A:m6A RNA rRNA 1618 LSU-23S Prokaryotic Cytosol 18021804   

Alpha Fold Predicted Structure:






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Protein sequence:

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

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-P75782-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P75782-F1.cif  
DSSP Secondary Structures   P75782.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The ybiN gene of Escherichia coli encodes adenine-N6 methyltransferase specific for modification of A1618 of 23 S ribosomal RNA, a methylated residue located close to the ribosomal exit tunnel. Sergiev PV, Serebryakova MV, Bogdanov AA, Dontsova OA J Mol Biol [details] 18021804 -