Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA wyosine derivatives biosynthesis protein Taw2
GI: 74570968
Orf: PH0793
COG: COG2520
UniProt: O58523
Structures: | 3A25 | 3A26 |
Alpha Fold Predicted Structure: AF-O58523-F1
Enzyme type: Alpha-amino-alpha-carboxypropyltransferase


PDB Structures:


3A25

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

S-adenosylmethionine (AdoMet) is a methyl donor used by a wide variety of methyltransferases, and it is also used as the source of an alpha-amino-alpha-carboxypropyl ("acp") group by several enzymes. tRNA-yW synthesizing enzyme-2 (TYW2) is involved in the biogenesis of a hypermodified nucleotide, wybutosine (yW), and it catalyzes the transfer of the "acp" group from AdoMet to the C7 position of the imG-14 base, a yW precursor. This modified nucleoside yW is exclusively located at position 37 of eukaryotic tRNA(Phe), and it ensures the anticodon-codon pairing on the ribosomal decoding site. Although this "acp" group has a significant role in preventing decoding frame shifts, the mechanism of the "acp" group transfer by TYW2 remains unresolved. Here we report the crystal structures and functional analyses of two archaeal homologs of TYW2 from Pyrococcus horikoshii and Methanococcus jannaschii. The in vitro mass spectrometric and radioisotope-labeling analyses confirmed that these archaeal TYW2 homologues have the same activity as yeast TYW2. The crystal structures verified that the archaeal TYW2 contains a canonical class-I methyltransferase (MTase) fold. However, their AdoMet-bound structures revealed distinctive AdoMet-binding modes, in which the "acp" group, instead of the methyl group, of AdoMet is directed to the substrate binding pocket. Our findings, which were confirmed by extensive mutagenesis studies, explain why TYW2 transfers the "acp" group, and not the methyl group, from AdoMet to the nucleobase.

Download RCSB-PDB Structures:

Pdb Files   3A25.pdb   3A26.pdb  
Pdbx/mmCIF Files   3A25.cif   3A26.cif  


Protein sequence:

MRTQGIKPRIREILSKELPEELVKLLPKRWVRIGDVLLLPLRPELEPYKHRIAEVYAEVLGVKTVLRKGHIHGETRKPDYELLYGSDTVTVHVENGIKYKLDVAKIMFSPANVKERVRMAKVAKPDELVVDMFAGIGHLSLPIAVYGKAKVIAIEKDPYTFKFLVENIHLNKVEDRMSAYNMDNRDFPGENIADRILMGYVVRTHEFIPKALSIAKDGAIIHYHNTVPEKLMPREPFETFKRITKEYGYDVEKLNELKIKRYAPGVWHVVLDLRVFKS

Comments:

Homologue of yeast Tyw2. It catalyzes the transfer of the “acp” group from AdoMet to the C7 position of the imG-14 base, forming yW-86. It was shown to act on tRNAPhe from yeast mutant strain which possess imG-14 in position 37.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
imG-14:yW-86 RNA tRNA 37 #AA #AA tRNAPhe-imG14#AA anticodon-loop Prokaryotic Cytosol 19717466   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-O58523-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-O58523-F1.cif  
DSSP Secondary Structures   O58523.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Biosynthesis of wyosine derivatives in tRNA: an ancient and highly diverse pathway in Archaea. de Crecy-Lagard V, Brochier-Armanet C, Urbonavicius J, Fernandez B, Phillips G, Lyons B, Noma A, Alvarez S, Droogmans L, Armengaud J, Grosjean H Mol Biol Evol [details] 20382657 -
Structural basis of AdoMet-dependent aminocarboxypropyl transfer reaction catalyzed by tRNA-wybutosine synthesizing enzyme, TYW2. Umitsu M, Nishimasu H, Noma A, Suzuki T, Ishitani R, Nureki O Proc Natl Acad Sci U S A [details] 19717466 -