Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (uracil(54)-C(5))-methyltransferase
Synonym: PYRAB10780
GI: 14521283
Orf: PAB0719
COG: COG2265
UniProt: Q9UZR7
Structures: | 2VS1 | 2JJQ |
Alpha Fold Predicted Structure: AF-Q9UZR7-F1
Enzyme type: methyltransferase
Position of modification - modification: t:54 - m5U


PDB Structures:


2VS1

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The 5-methyluridine is invariably found at position 54 in the TPsiC loop of tRNAs of most organisms. In Pyrococcus abyssi, its formation is catalyzed by the S-adenosyl-l-methionine-dependent tRNA (uracil-54, C5)-methyltransferase ((Pab)TrmU54), an enzyme that emerged through an ancient horizontal transfer of an RNA (uracil, C5)-methyltransferase-like gene from bacteria to archaea. The crystal structure of (Pab)TrmU54 in complex with S-adenosyl-l-homocysteine at 1.9 A resolution shows the protein organized into three domains like Escherichia coli RumA, which catalyzes the same reaction at position 1939 of 23S rRNA. A positively charged groove at the interface between the three domains probably locates part of the tRNA-binding site of (Pab)TrmU54. We show that a mini-tRNA lacking both the D and anticodon stem-loops is recognized by (Pab)TrmU54. These results were used to model yeast tRNA(Asp) in the (Pab)TrmU54 structure to get further insights into the different RNA specificities of RumA and (Pab)TrmU54. Interestingly, the presence of two flexible loops in the central domain, unique to (Pab)TrmU54, may explain the different substrate selectivities of both enzymes. We also predict that a large TPsiC loop conformational change has to occur for the flipping of the target uridine into the (Pab)TrmU54 active site during catalysis.

Download RCSB-PDB Structures:

Pdb Files   2JJQ.pdb   2VS1.pdb  
Pdbx/mmCIF Files   2JJQ.cif   2VS1.cif  


Protein sequence:

MRGVIRKLNDDGFGVLKGILVPFSAPGDEIIVERVERVKKRRVASQWKLVRSSPLRVGPRCKAFGKCGGCTLQHLNYDYQLEFKRKKLKRILGFEVEVVPSPKIFGHRNRIDLAITKDGIGFRERGKWWKIVDIDECPVFGKTSREAIERLKEFIEEEKISVWNIKKDEGFLRYMVLREGKFTEEVMVNFVTKEGNLPDPTNYFDFDSIYWSVNRSKSDVSYGDIERFWGKEFIRERLDDVDYLIHPNSFFQTNSYQAVNLVRKVSELVEGEKILDMYSGVGTFGIYLAKRGFNVKGFDSNEFAIEMARRNVEINNVDAEFEVASDREVSVKGFDTVIVDPPRAGLHPRLVKRLNREKPGVIVYVSCNPETFARDVKMLDYRIDEIVALDMFPHTPHVELVAKLV

Comments:

The activity was tested in vitro on yeast tRNAAsp transcript




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
U:m5U RNA tRNA 54 GUC GUC tRNAAspGUC TΨC-loop Prokaryotic Cytosol 18069966   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-Q9UZR7-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q9UZR7-F1.cif  
DSSP Secondary Structures   Q9UZR7.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity. Walbott H, Leulliot N, Grosjean H, Golinelli-Pimpaneau B Nucleic Acids Res [details] 18653523 -
Acquisition of a bacterial RumA-type tRNA(uracil-54, C5)-methyltransferase by Archaea through an ancient horizontal gene transfer. Urbonavicius J, Auxilien S, Walbott H, Trachana K, Golinelli-Pimpaneau B, Brochier-Armanet C, Grosjean H Mol Microbiol [details] 18069966 -

Links:

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