Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA(pseudouridine54-N1)-methyltransferase
Synonym: MJ1640
GI: 15669836
COG: COG1901
UniProt: Q59034
Structures: | 3AI9 | 3AIA |
Alpha Fold Predicted Structure: AF-Q59034-F1
Enzyme type: methyltransferase
Position of modification - modification: t:54 - m1Y


PDB Structures:


3AI9

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The proteins in DUF358 family are all bacterial proteins, which are ∼200 amino acids long with unknown function. Bioinformatics analysis suggests that these proteins contain several conserved arginines and aspartates that might adopt SPOUT-class fold. Here we report crystal structure of Methanocaldococcus jannaschii DUF358/Mj1640 in complex with S-adenosyl-L-methionine (SAM) at 1.4 Å resolution. The structure reveals a single domain structure consisting of eight-stranded β-sheets sandwiched by six α-helices at both sides. Similar to other SPOUT-class members, Mj1640 contains a typical deep trefoil knot at its C-terminus to accommodate the SAM cofactor. However, Mj1640 has limited structural extension at its N-terminus, which is unique to this family member. Mj1640 forms a dimer, which is mediated by two parallel pairs of α-helices oriented almost perpendicular to each other. Although Mj1640 shares close structural similarity with Nep1, the significant differences in N-terminal extension domain and the overall surface charge distribution strongly suggest that Mj1640 might target a different RNA sequence. Detailed structural analysis of the SAM-binding pocket reveals that Asp157 or Glu183 from its own monomer or Ser43 from the associate monomer probably plays the catalytic role for RNA methylation.

Download RCSB-PDB Structures:

Pdb Files   3AI9.pdb   3AIA.pdb  
Pdbx/mmCIF Files   3AI9.cif   3AIA.cif  


Protein sequence:

MREFIFKANKTITSSDINLKDLPGSCGRLDLLCRCVSDAFFLSHDIRRDVVFYAVLYGQPNPPVCIKFVGSELKKVSPDERNIAIFIKKALKKFEELDEEQRKDWNQSTPGIYVRRLGFRNLVLEKLEEGKNIYYLHMNGEDVENVDIENPVFIIGDHIGIGEEDERFLDEIKAKRISLSPLELHANHCITIIHNVLDKKRICEI

Comments:

AdoMet dependent methyltransferase. It was shown to catalyze Y:m1Y reaction in vitro in position 54 of a synthetic substrate resembling tRNATrp. Requires pseudouridine (or possibly uridine) in position 55 for efficient conversion of Y54 to m1Y54. This modification is located in the T-loop and is important for the tertiary structure of the tRNA molecule.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
Y:m1Y tRNA (t)   54 22274954   

Alpha Fold Predicted Structure:






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Protein sequence:

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

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-Q59034-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q59034-F1.cif  
DSSP Secondary Structures   Q59034.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The archaeal COG1901/DUF358 SPOUT-methyltransferase members, together with pseudouridine synthase Pus10, catalyze the formation of 1-methylpseudouridine at position 54 of tRNA. Chatterjee K, Blaby IK, Thiaville PC, Majumder M, Grosjean H, Yuan YA, Gupta R, de Crécy-Lagard V RNA [details] 22274953 -
Identification of the enzyme responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs. Wurm JP, Griese M, Bahr U, Held M, Heckel A, Karas M, Soppa J, Wöhnert J RNA [details] 22274954 -
Crystal structure of Mj1640/DUF358 protein reveals a putative SPOUT-class RNA methyltransferase. Chen HY, Yuan YA J Mol Cell Biol [details] 21098051 -