Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (cytidine(32)-2′-O)-methyltransferase
Synonym: Saci_0621
GI: 70606436
COG: COG0565
UniProt: Q4JB16
Structures: | 4CNF | 4CNG |
Alpha Fold Predicted Structure: AF-Q4JB16-F1
Enzyme type: methyltransferase
Position of modification - modification: t:32 - Cm


PDB Structures:


4CNF

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   4CNF.pdb   4CNG.pdb  
Pdbx/mmCIF Files   4CNF.cif   4CNG.cif  


Protein sequence:

MTIRLVIVEPEGAYNLGFIARLVKNFLIDEFYVVNPKCDINEAIKFSAKGSEVIEKMMKITNNFDDAIRDVDLKIATSSIADIKGDLLRKSIRPIDLERLIKDKKVAFIFGRESVGLTREEIAKSDFLLFIPANPEYPVLNLSHAVGIVLYELWRNRDNKVPTVSSEPIKLIDDYSKKITDILVNKEATKSMYLVLKRVLIKGIEDNEEAMTIVRILRKIYVRLAKKENESDKLL

Comments:

Homolog of E. coli TrmJ. While the four canonical nucleosides are substrates of the Escherichia coli enzyme, the archaeal TrmJ can only methylate the ribose of a cytidine.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
C:Cm tRNA (t) 32 24951554   

Alpha Fold Predicted Structure:






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Protein sequence:

M T I R L V I V E P E G A Y N L G F I A R L V K N F L I D E F Y V V N P K C D I N E A I K F S A K G S E V I E K M M K I T N N F D D A I R D V D L K I A T S S I A D I K G D L L R K S I R P I D L E R L I K D K K V A F I F G R E S V G L T R E E I A K S D F L L F I P A N P E Y P V L N L S H A V G I V L Y E L W R N R D N K V P T V S S E P I K L I D D Y S K K I T D I L V N K E A T K S M Y L V L K R V L I K G I E D N E E A M T I V R I L R K I Y V R L A K K E N E S D K L 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-Q4JB16-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q4JB16-F1.cif  
DSSP Secondary Structures   Q4JB16.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
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 -

Links:

_PubMed_