Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (adenine(9)-N1)-methyltransferase
UniProt: Q4J894
Structures: | 5A7T | 5A7Y | 5A7Z |
Alpha Fold Predicted Structure: AF-Q4J894-F1
Enzyme type: methyltransferase


PDB Structures:


5A7T

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Purine nucleosides on position 9 of eukaryal and archaeal tRNAs are frequently modified in vivo by the post-transcriptional addition of a methyl group on their N1 atom. The methyltransferase Trm10 is responsible for this modification in both these domains of life. While certain Trm10 orthologues specifically methylate either guanosine or adenosine at position 9 of tRNA, others have a dual specificity. Until now structural information about this enzyme family was only available for the catalytic SPOUT domain of Trm10 proteins that show specificity toward guanosine. Here, we present the first crystal structure of a full length Trm10 orthologue specific for adenosine, revealing next to the catalytic SPOUT domain also N- and C-terminal domains. This structure hence provides crucial insights in the tRNA binding mechanism of this unique monomeric family of SPOUT methyltransferases. Moreover, structural comparison of this adenosine-specific Trm10 orthologue with guanosine-specific Trm10 orthologues suggests that the N1 methylation of adenosine relies on additional catalytic residues.

Download RCSB-PDB Structures:

Pdb Files   5A7T.pdb   5A7Y.pdb   5A7Z.pdb  
Pdbx/mmCIF Files   5A7T.cif   5A7Y.cif   5A7Z.cif  


Protein sequence:

MTLAKVFSQKLRELGISSIYIGHERPSLQSLAIKMLLKNYGLVEERREGMLITQDHGIKLISGKGTETSRYTFRKGGKKVSIHLPEYPKMVIDLGLFEFLNEEEKEKTLLQVDLCLSVIRKFLWDGNLTVVGKADYVLGRANIVQSLSLSDEDNPVILDPYGDVVATDQILRDHNVFVIGGIVDKGRRLDRATERLALSRGYSFPRVKIQLRGSIIGVPDEINKILEIILRVKELDQSLEEAIISLQSKSDKISRLLHDVQLYGMEVLEEEARWLRADDKVIEIVRSRLGKN

Comments:





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q4J894-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q4J894-F1.cif  
DSSP Secondary Structures   Q4J894.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Structural and functional insights into tRNA binding and adenosine N1-methylation by an archaeal Trm10 homologue. Van Laer B, Roovers M, Wauters L, Kasprzak JM, Dyzma M, Deyaert E, Kumar Singh R, Feller A, Bujnicki JM, Droogmans L, Versées W Nucleic Acids Res. [details] 26673726 10.1093/nar/gkv1369