Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (cytidine(34)-2′-O)-methyltransferase
Synonym: YibK
GI: 16131477
Orf: b3606, JW3581
COG: COG0219
UniProt: P0AGJ7
Structures: | 4JAK | 4JAL |
Alpha Fold Predicted Structure: AF-P0AGJ7-F1
Enzyme type: methyltransferase
Position of modification - modification: t:34 - Cm
t:34 - cmnm5Um


PDB Structures:


4JAK

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Unlike other transfer RNAs (tRNA)-modifying enzymes from the SPOUT methyltransferase superfamily, the tRNA (Um34/Cm34) methyltransferase TrmL lacks the usual extension domain for tRNA binding and consists only of a SPOUT domain. Both the catalytic and tRNA recognition mechanisms of this enzyme remain elusive. By using tRNAs purified from an Escherichia coli strain with the TrmL gene deleted, we found that TrmL can independently catalyze the methyl transfer from S-adenosyl-L-methionine to and isoacceptors without the involvement of other tRNA-binding proteins. We have solved the crystal structures of TrmL in apo form and in complex with S-adenosyl-homocysteine and identified the cofactor binding site and a possible active site. Methyltransferase activity and tRNA-binding affinity of TrmL mutants were measured to identify residues important for tRNA binding of TrmL. Our results suggest that TrmL functions as a homodimer by using the conserved C-terminal half of the SPOUT domain for catalysis, whereas residues from the less-conserved N-terminal half of the other subunit participate in tRNA recognition.

Download RCSB-PDB Structures:

Pdb Files   4JAK.pdb   4JAL.pdb  
Pdbx/mmCIF Files   4JAK.cif   4JAL.cif  


Protein sequence:

MLNIVLYEPEIPPNTGNIIRLCANTGFRLHIIEPMGFAWDDKRLRRAGLDYHEFTAVTRHHDYRAFLEAENPQRLFALTTKGTPAHSAVSYQDGDYLMFGPETRGLPASILDALPAEQKIRIPMVPDSRSMNLSNAVSVVVYEAWRQLGYPGAVLRD

Comments:

This small SAM-dependent methyltransferase (157 amino acids) exists as an homodimer. It acts on the ribose of the wobble U or C34 of E. coli tRNALeu harboring an i6A37 modification in the anticodon loop. It allows increasing the performance of the tRNA reading the corresponding complementary codons. The enzyme is not essential for cell viability. Belongs to the SPOUT-type TrmH/TrmL subfamily.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:Um RNA tRNA 34 UAA JAA tRNAPheUAA wobble - position Prokaryotic Cytosol 20855540   
C:Cm RNA tRNA 34 CAA BAA tRNALeuBAA wobble - position Prokaryotic Cytosol 20855540   
cmnm5U:cmnm5Um RNA tRNA 34 !AA )AA tRNALeu)AA wobble - position Prokaryotic Cytosol

Alpha Fold Predicted Structure:






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Protein sequence:

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

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-P0AGJ7-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P0AGJ7-F1.cif  
DSSP Secondary Structures   P0AGJ7.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Enzymology of tRNA modification in the bacterial MnmEG pathway. Armengod ME, Moukadiri I, Prado S, Ruiz-Partida R, Benitez-Paez A, Villarroya M, Lomas R, Garzon MJ, Martinez-Zamora A, Meseguer S, Navarro-Gonzalez C Biochimie [details] 22386868 -
YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors. Benitez-Paez A, Villarroya M, Douthwaite S, Gabaldon T, Armengod ME RNA [details] 20855540 -
The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL. Liu RJ, Zhou M, Fang ZP, Wang M, Zhou XL, Wang ED... Nucleic Acids Res [details] 23804755 -
Identification of determinants for tRNA substrate recognition by Escherichia coli C/U34 2'-O-methyltransferase. Zhou M, Long T, Fang ZP, Zhou XL, Liu RJ, Wang ED RNA Biol. [details] 26106808 10.1080/15476286.2015.1050576

Links:

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