Modomics - A Database of RNA Modifications

ID Card:

Full name: DNA (cytosine-5)-methyltransferase
Synonym: DNA -methyltransferase
GI: 74852778
UniProt: Q54JH6
Alpha Fold Predicted Structure: AF-Q54JH6-F1
Enzyme type: methyltransferase
Position of modification - modification: t:38 - m5C



Protein sequence:

MEQLRVLEFYSGIGGMHYGLQESGVDFQVIQSFDINTNANLNYKYTFNEDSSQKSIESYSVEELEGFKANAWLMSPPCQPFTRLGLQKDDQDNRTNSFFHLLDVLTKIKDPPTYILIENVFGFAKKGSSNTRDHLLDTLIKMNYSFQEFHLSPQQFGLANQRLRYFCIAKRNGKLNFKKEQDKHNEKVDENKLNNNSNNNNEQNKYDNLKILDHIPGYDFHTTLEECDEISNYFDKDLTDDELYEKYKVPHNLLLSKGMLFDIKQKDSKTSNCVTKSYGKFIEGTGSIIQMDNNFKADINDNKSLIPLKLRYFSPKEITRLHGFPEEFKFSPKLTTIQCYRLIGNSLNVKIVSELLKVLVSPNEEEEQQEQQKEKEGKK

Comments:

Dnmt2 is a member of the eukaryotic DNA methyltransferase family. A few model organisms, especially Drosophila melanogaster, Schizosaccharomyces pombe, Entamoeba histolytica and Dictyostelium discoideum contain only one Dnmt2 homologue but lack the more active homologues Dnmt1 and Dnmt3 (Müller et al. 2013 ). D.discoideum Dnmt2-homologue DnmA is an active tRNA methyltransferase that modifies C38 in tRNAGUCAsp in vitro and in vivo. By an ultraviolet-crosslinking and immunoprecipitation approach, we identified further DnmA targets. This revealed specific tRNA fragments bound by the enzyme and identified tRNA(CUC/UUC)Glu and tRNAGCCGly as new but weaker substrates for both human Dnmt2 and DnmA in vitro but apparently not in vivo. Dnmt2 enzymes form transient covalent complexes with their substrates (Müller et al. 2013 ).




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
C:m5C RNA tRNA 38 CUC CUC tRNAGluCUC anticodon-loop Cytoplasm 23877245   
C:m5C RNA tRNA 38 UUC UUC tRNAGluUUC anticodon-loop Cytoplasm 23877245   
C:m5C RNA tRNA 38 GCC GCC tRNAGlyGCC anticodon-loop Cytoplasm 23877245   
C:m5C RNA tRNA 38 GUC GUC tRNAAspGUC anticodon-loop Cytoplasm 23877245   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q54JH6-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q54JH6-F1.cif  
DSSP Secondary Structures   Q54JH6.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Dynamic modulation of Dnmt2-dependent tRNA methylation by the micronutrient queuine. Müller M, Hartmann M, Schuster I, Bender S, Thüring KL, Helm M, Katze JR, Nellen W, Lyko F, Ehrenhofer-Murray AE. Nucleic Acids Res. [details] 26424849 10.1093/nar/gkv980