Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal RNA large subunit methyltransferase O
Synonym: TTHA1493
GI: 55981462
COG: COG1092
UniProt: Q5SI81
Structures: | 4DMG |
Alpha Fold Predicted Structure: AF-Q5SI81-F1
Enzyme type: methyltransferase
Position of modification - modification: l:1964(1942) - m5C


PDB Structures:


4DMG

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Methylation of cytidines at carbon-5 is a common posttranscriptional RNA modification encountered across all domains of life. Here, we characterize the modifications of C1942 and C1962 in Thermus thermophilus 23 S rRNA as 5-methylcytidines (m(5)C) and identify the two associated methyltransferases. The methyltransferase modifying C1942, named RlmO, has not been characterized previously. RlmO modifies naked 23 S rRNA, but not the assembled 50 S subunit or 70 S ribosomes. The x-ray crystal structure of this enzyme in complex with the S-adenosyl-l-methionine cofactor at 1.7 Å resolution confirms that RlmO is structurally related to other m(5)C rRNA methyltransferases. Key residues in the active site are located similar to the further distant 5-methyluridine methyltransferase RlmD, suggestive of a similar enzymatic mechanism. RlmO homologues are primarily found in mesophilic bacteria related to T. thermophilus. In accordance, we find that growth of the T. thermophilus strain with an inactivated C1942 methyltransferase gene is not compromised at non-optimal temperatures.

Download RCSB-PDB Structures:

Pdb Files   4DMG.pdb  
Pdbx/mmCIF Files   4DMG.cif  


Protein sequence:

MLGPVLRLVVKAGKERKLRNFYPNLYRDEIAAPPEGVGVAEAVDAEGHFLAVGYYDPRSRVPFRAFRFDPGPLNRAFFQGRFARALRRRQGLGESHRLVHGEADGLPGLVVDRFGEVLVLQVRSRGMEALREVWLPALLEVVAPKGVYERSDVEARRQEGLPERVGVVYGEVPEVLEVEEDGLRFPIPLALAQKTGYYLDQRENRRLFEAMVRPGERVLDVYSYVGGFALRAARKGAYALAVDKDLEALGVLDQAALRLGLRVDIRHGEALPTLRGLEGPFHHVLLDPPTLVKRPEELPAMKRHLVDLVREALRLLAEEGFLWLSSCSYHLRLEDLLEVARRAAADLGRRLRVHRVTYQPEDHPWSLHIPESLYLKTLVLQDDPL

Comments:

RlmO modifies naked 23 S rRNA, but not the assembled 50 S subunit or 70 S ribosomes.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
C:m5C rRNA (r) LSU/23S/prokaryotic cytosol 1964 22711535   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q5SI81-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q5SI81-F1.cif  
DSSP Secondary Structures   Q5SI81.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Identification and characterization of the Thermus thermophilus 5-methylcytidine (m5C) methyltransferase modifying 23 S ribosomal RNA (rRNA) base C1942. Larsen LH, Rasmussen A, Giessing AM, Jogl G, Kirpekar F... J Biol Chem [details] 22711535 -

Links:

_PubMed_