Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (cytidine(32)/uridine(32)-2′-O)-methyltransferase
Synonym: YfhQ, JW2516
GI: 83287928
Orf: b2532
COG: COG0565
UniProt: P0AE01
Structures: | 4CND | 4CNE | 4XBO |
Alpha Fold Predicted Structure: AF-P0AE01-F1
Enzyme type: methyltransferase
Position of modification - modification: t:32 - Um
t:32 - Cm


PDB Structures:


4CND

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The 2'-O-methylation of the nucleoside at position 32 of tRNA is found in organisms belonging to the three domains of life. Unrelated enzymes catalyzing this modification in Bacteria (TrmJ) and Eukarya (Trm7) have already been identified, but until now, no information is available for the archaeal enzyme. In this work we have identified the methyltransferase of the archaeon Sulfolobus acidocaldarius responsible for the 2'-O-methylation at position 32. This enzyme is a homolog of the bacterial TrmJ. Remarkably, both enzymes have different specificities for the nature of the nucleoside at position 32. While the four canonical nucleosides are substrates of the Escherichia coli enzyme, the archaeal TrmJ can only methylate the ribose of a cytidine. Moreover, the two enzymes recognize their tRNA substrates in a different way. We have solved the crystal structure of the catalytic domain of both enzymes to gain better understanding of these differences at a molecular level.

Download RCSB-PDB Structures:

Pdb Files   4CND.pdb   4CNE.pdb   4XBO.pdb  
Pdbx/mmCIF Files   4CND.cif   4CNE.cif   4XBO.cif  


Protein sequence:

MLQNIRIVLVETSHTGNMGSVARAMKTMGLTNLWLVNPLVKPDSQAIALAAGASDVIGNAHIVDTLDEALAGCSLVVGTSARSRTLPWPMLDPRECGLKSVAEAANTPVALVFGRERVGLTNEELQKCHYHVAIAANPEYSSLNLAMAVQVIAYEVRMAWLATQENGEQVEHEETPYPLVDDLERFYGHLEQTLLATGFIRENHPGQVMNKLRRLFTRARPESQELNILRGILASIEQQNKGNKAE

Comments:

AdoMet is the methyl group donor.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
C:Cm RNA tRNA 32 UGA UGA tRNASerUGA anticodon loop Prokaryotic Cytosol
C:Cm RNA tRNA 32 CUG CUG tRNAGlnCUG anticodon loop Prokaryotic Cytosol
U:Um RNA tRNA 32 UGA UGA tRNASerUGA anticodon loop Prokaryotic Cytosol
U:Um RNA tRNA 32 CUG CUG tRNAGlnCUG anticodon loop Prokaryotic Cytosol

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P0AE01-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P0AE01-F1.cif  
DSSP Secondary Structures   P0AE01.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase. Purta E, van Vliet F, Tkaczuk KL, Dunin-Horkawicz S, Mori H, Droogmans L, Bujnicki JM BMC Mol Biol [details] 16848900 -
Characterization of two homologous 2'-O-methyltransferases showing different specificities for their tRNA substrates. Somme J, Van Laer B, Roovers M, Steyaert J, Versees W, Droogmans L... RNA [details] 24951554 -
tRNA recognition by a bacterial tRNA Xm32 modification enzyme from the SPOUT methyltransferase superfamily. Liu RJ, Long T, Zhou M, Zhou XL, Wang ED Nucleic Acids Res. [details] 26202969 10.1093/nar/gkv745