5YRT
Diol dehydratase, AdoCbl/substrate-free, anaerobically-prepared crystal
Summary for 5YRT
| Entry DOI | 10.2210/pdb5yrt/pdb |
| Descriptor | Diol dehydrase alpha subunit, Diol dehydrase beta subunit, Diol dehydrase gamma subunit, ... (9 entities in total) |
| Functional Keywords | adenosylcobalamin, radical enzyme, lyase |
| Biological source | Klebsiella oxytoca More |
| Total number of polymer chains | 12 |
| Total formula weight | 398191.94 |
| Authors | Shibata, N. (deposition date: 2017-11-10, release date: 2018-09-19, Last modification date: 2023-11-22) |
| Primary citation | Shibata, N.,Sueyoshi, Y.,Higuchi, Y.,Toraya, T. Direct Participation of a Peripheral Side Chain of a Corrin Ring in Coenzyme B12Catalysis. Angew. Chem. Int. Ed. Engl., 57:7830-7835, 2018 Cited by PubMed Abstract: The crystal structures of the B -dependent isomerases (eliminating) diol dehydratase and ethanolamine ammonia-lyase complexed with adenosylcobalamin were solved with and without substrates. The structures revealed that the peripheral a-acetamide side chain of the corrin ring directly interacts with the adenosyl group to maintain the group in the catalytic position, and that this side chain swings between the original and catalytic positions in a synchronized manner with the radical shuttling between the coenzyme and substrate/product. Mutations involving key residues that cooperatively participate in the positioning of the adenosyl group, directly or indirectly through the interaction with the a-side chain, decreased the turnover rate and increased the relative rate of irreversible inactivation caused by undesirable side reactions. These findings guide the engineering of enzymes for improved catalysis and producing useful chemicals by utilizing the high reactivity of radical species. PubMed: 29797764DOI: 10.1002/anie.201803591 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.7 Å) |
Structure validation
Download full validation report
