Modomics - A Database of RNA Modifications

ID Card:

Full name: Methylenetetrahydrofolate-tRNA-(uracil-54-)-methyltransferase TrmFO
GI: 55981411
COG: COG1206
UniProt: Q5SID2
Structures: | 3G5Q | 3G5R | 3G5S |
Alpha Fold Predicted Structure: AF-Q5SID2-F1
Enzyme type: methyltransferase
Position of modification - modification: t:54 - m5s2U


PDB Structures:


3G5Q

Structure Description:

Title: Crystal structure of Thermus thermophilus TrmFO
Classification: TRANSFERASE
Technique: X-Ray Diffraction
Resolution: 2.1
R value free: 0.2
R value observed: 0.152
R value work: 0.149

Abstract of the PDB Structure's related Publication:

tRNAs from all 3 phylogenetic domains have a 5-methyluridine at position 54 (T54) in the T-loop. The methyl group is transferred from S-adenosylmethionine by TrmA methyltransferase in most Gram-negative bacteria and some archaea and eukaryotes, whereas it is transferred from 5,10-methylenetetrahydrofolate (MTHF) by TrmFO, a folate/FAD-dependent methyltransferase, in most Gram-positive bacteria and some Gram-negative bacteria. However, the catalytic mechanism remains unclear, because the crystal structure of TrmFO has not been solved. Here, we report the crystal structures of Thermus thermophilus TrmFO in its free form, tetrahydrofolate (THF)-bound form, and glutathione-bound form at 2.1-, 1.6-, and 1.05-A resolutions, respectively. TrmFO consists of an FAD-binding domain and an insertion domain, which both share structural similarity with those of GidA, an enzyme involved in the 5-carboxymethylaminomethylation of U34 of some tRNAs. However, the overall structures of TrmFO and GidA are basically different because of their distinct domain orientations, which are consistent with their respective functional specificities. In the THF complex, the pteridin ring of THF is sandwiched between the flavin ring of FAD and the imidazole ring of a His residue. This structure provides a snapshot of the folate/FAD-dependent methyl transfer, suggesting that the transferring methylene group of MTHF is located close to the redox-active N5 atom of FAD. Furthermore, we established an in vitro system to measure the methylation activity. Our TrmFO-tRNA docking model, in combination with mutational analyses, suggests a catalytic mechanism, in which the methylene of MTHF is directly transferred onto U54, and then the exocyclic methylene of U54 is reduced by FADH(2).

Download RCSB-PDB Structures:

Pdb Files   3G5Q.pdb   3G5R.pdb   3G5S.pdb  
Pdbx/mmCIF Files   3G5Q.cif   3G5R.cif   3G5S.cif  


Protein sequence:

MERVNVVGAGLAGSEAAWTLLRLGVPVRLFEMRPKRMTPAHGTDRFAEIVCSNSLGGEGETNAKGLLQAEMRRAGSLVMEAADLARVPAGGALAVDREEFSGYITERLTGHPLLEVVREEVREIPPGITVLATGPLTSEALAEALKRRFGDHFLAYYDAASPIVLYESIDLTKCFRAGRYGQSADYLNCPMTEEEYRRFHQALLEAQRHTPHDWEKLEFFEACVPVEELARRGYQTLLFGPMKPVGLVDPRTGKEPFAVVQLRQEDKAGRMWSLVGFQTGLKWPEQKRLIQMIPGLENAEIVRYGVMHRNTYLNAPRLLGETLEFREAEGLYAAGVLAGVEGYLESAATGFLAGLNAARKALGLPPVAPPEESMLGGLVRYLATANPEGFQPMYANWGLVPPVEGRMGKKEKRQAMYRRGLEAFSAWLSGLNPPLPRPEAALV

Comments:

Homologue of B. subtilis TrmFO responsible for m5U formation in tRNA position 54. In T. thermophilus m5U in position 54 is further processed to m5s2U. Crystal structures of Thermus thermophilus TrmFO in its free form, tetrahydrofolate (THF)-bound form, and glutathione-bound form at 2.1-, 1.6-, and 1.05-A resolutions were solved. The activity was tested in vitro on tRNAIle transcript.





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M E R V N V V G A G L A G S E A A W T L L R L G V P V R L F E M R P K R M T P A H G T D R F A E I V C S N S L G G E G E T N A K G L L Q A E M R R A G S L V M E A A D L A R V P A G G A L A V D R E E F S G Y I T E R L T G H P L L E V V R E E V R E I P P G I T V L A T G P L T S E A L A E A L K R R F G D H F L A Y Y D A A S P I V L Y E S I D L T K C F R A G R Y G Q S A D Y L N C P M T E E E Y R R F H Q A L L E A Q R H T P H D W E K L E F F E A C V P V E E L A R R G Y Q T L L F G P M K P V G L V D P R T G K E P F A V V Q L R Q E D K A G R M W S L V G F Q T G L K W P E Q K R L I Q M I P G L E N A E I V R Y G V M H R N T Y L N A P R L L G E T L E F R E A E G L Y A A G V L A G V E G Y L E S A A T G F L A G L N A A R K A L G L P P V A P P E E S M L G G L V R Y L A T A N P E G F Q P M Y A N W G L V P P V E G R M G K K E K R Q A M Y R R G L E A F S A W L S G L N P P L P R P E A A L V
50100150200250300350400SequenceGHTBSN

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-Q5SID2-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q5SID2-F1.cif  
DSSP Secondary Structures   Q5SID2.dssp  





Publications: