9TZH

X-ray structure of S. cerevisiae threonlycarbamoyladenosine dehydratase 1 (residues 50-429) in complex with AMP at 3.7 A resolution

Summary for 9TZH

• Entry DOI: 10.2210/pdb9tzh/pdb
• Related: 9HMP
• Descriptor: tRNA threonylcarbamoyladenosine dehydratase 1, ADENOSINE MONOPHOSPHATE, MAGNESIUM ION (3 entities in total)
• Functional Keywords: threonlycarbamoyladenosine dehydratase, t6a, ct6a, modification, trna, rna binding protein
• Biological source: Saccharomyces cerevisiae (brewer's yeast)
• Total number of polymer chains: 4
• Total formula weight: 175597.88

Authors

Hirschmann, J.,Huber, E.M. (deposition date: 2026-01-22, release date: 2026-04-01, Last modification date: 2026-05-27)

Primary citation

Hirschmann, J.,Sonntag, R.,Heiss, M.,Wegrzyn, E.,Heinemeyer, W.,Carell, T.,Huber, E.M.
Structural and biochemical characterization of yeast Tcd enzymes installing the post-transcriptional modification ct6A in tRNA.
Nucleic Acids Res., 54:-, 2026

PubMed Abstract: Post-transcriptional modifications near the anticodon of transfer ribonucleic acids (tRNAs) ensure translation fidelity and accuracy. For instance, at position 37, the universally conserved and essential nucleoside N6-threonylcarbamoyladenosine (t6A) supports decoding of ANN triplets. In some organisms t6A is converted to cyclic t6A (ct6A), but only little is known about this ATP-dependent reaction and the corresponding threonylcarbamoyladenosine dehydratases (Tcds). We here show that yeast Tcds localize to the outer mitochondrial membrane and co-purify with tRNAs recognizing ANN codons. Depending on the number of TCD genes in the genome, the proteins form V-shaped hetero- or homodimers, of which at least one subunit binds and modifies tRNAs. The C-terminal, monomeric domain shares similarities with Cas9-endonucleases and assists tRNA recognition, while the N-terminal domain mediates dimerization and contains the active site. Structure-based mutagenesis and activity assays imply that yeast Tcds lack a catalytic cysteine and do not covalently bind their substrate as proposed for Escherichia coli TcdA.

PubMed: 42087783
DOI: 10.1093/nar/gkag376

Experimental method

X-RAY DIFFRACTION (3.7 Å)