8RAF
Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis point mutant R90I (holo form)
Summary for 8RAF
| Entry DOI | 10.2210/pdb8raf/pdb |
| Descriptor | Aminotransferase class IV, PYRIDOXAL-5'-PHOSPHATE (3 entities in total) |
| Functional Keywords | daat, point mutant, aminotransferase, transaminase, haliscomenobacter hydrossis, transferase |
| Biological source | Haliscomenobacter hydrossis DSM 1100 |
| Total number of polymer chains | 1 |
| Total formula weight | 32524.91 |
| Authors | Matyuta, I.O.,Bakunova, A.K.,Minyaev, M.E.,Popov, V.O.,Bezsudnova, E.Y.,Boyko, K.M. (deposition date: 2023-12-01, release date: 2023-12-27, Last modification date: 2024-05-08) |
| Primary citation | Bakunova, A.K.,Matyuta, I.O.,Minyaev, M.E.,Isaikina, T.Y.,Boyko, K.M.,Popov, V.O.,Bezsudnova, E.Y. Multifunctionality of arginine residues in the active sites of non-canonical d-amino acid transaminases. Arch.Biochem.Biophys., 756:110011-110011, 2024 Cited by PubMed Abstract: Structure-function relationships are key to understanding enzyme mechanisms, controlling enzyme activities, and designing biocatalysts. Here, we investigate the functions of arginine residues in the active sites of pyridoxal-5'-phosphate (PLP)-dependent non-canonical d-amino acid transaminases, focusing on the analysis of a transaminase from Haliscomenobacter hydrossis. Our results show that the tandem of arginine residues R28* and R90, which form the conserved R-[RK] motif in non-canonical d-amino acid transaminases, not only facilitates effective substrate binding but also regulates the catalytic properties of PLP. Non-covalent interactions between residues R28*, R90, and Y147 strengthen the hydrogen bond between Y147 and PLP, thereby maintaining the reactivity of the cofactor. Next, the R90 residue contributes to the stability of the holoenzyme. Finally, the R90I substitution induces structural changes that lead to substrate promiscuity, as evidenced by the effective binding of substrates with and without the α-carboxylate group. This study sheds light on the structural determinants of the activity of non-canonical d-amino acid transaminases. Understanding the structural basis of the active site plasticity in the non-canonical transaminase from H. hydrossis, which is characterized by effective conversion of d-amino acids and α-keto acids, may help to tailor it for industrial applications. PubMed: 38649133DOI: 10.1016/j.abb.2024.110011 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2 Å) |
Structure validation
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