9HMP
X-ray structure of S. cerevisiae threonylcarbamoyladenosine dehydratase 1 (residues 50-429) in complex with AMP
Summary for 9HMP
| Entry DOI | 10.2210/pdb9hmp/pdb |
| Related | 9HMO |
| Descriptor | tRNA threonylcarbamoyladenosine dehydratase 1, ADENOSINE MONOPHOSPHATE, CHLORIDE ION, ... (6 entities in total) |
| Functional Keywords | trna, modification, threonylcarbamoyladenosine dehydratase, cyclic n6-threonylcarbamoyladenosine, ct6a, yeast, rna binding protein |
| Biological source | Saccharomyces cerevisiae (brewer's yeast) |
| Total number of polymer chains | 4 |
| Total formula weight | 175953.94 |
| Authors | Hirschmann, J.,Huber, E.M. (deposition date: 2024-12-09, release date: 2025-12-24, 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 Cited by 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: 42087783DOI: 10.1093/nar/gkag376 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (4 Å) |
Structure validation
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