3G5Q

Crystal structure of Thermus thermophilus TrmFO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.102 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Atomic structure of a folate/FAD-dependent tRNA T54 methyltransferase

Nishimasu, H.Ishitani, R.Yamashita, K.Iwashita, C.Hirata, A.Hori, H.Nureki, O.

(2009) Proc.Natl.Acad.Sci.USA 106: 8180-8185

  • DOI: 10.1073/pnas.0901330106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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, where ...

    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).


    Organizational Affiliation

    Department of Basic Medical Science, Division of Structure Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase trmFO
A
443Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: trmFO
EC: 2.1.1.74
Find proteins for Q5SID2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SID2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
MRD
Query on MRD

Download SDF File 
Download CCD File 
A
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.102 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.149 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 68.355α = 90.00
b = 75.370β = 90.00
c = 156.089γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
MOLREPphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance