8ZB2
L-Methionine oxidase from Burkholderiales bacterium
Summary for 8ZB2
| Entry DOI | 10.2210/pdb8zb2/pdb |
| Descriptor | FAD-binding protein, FLAVIN-ADENINE DINUCLEOTIDE, THIOCYANATE ION (3 entities in total) |
| Functional Keywords | l-methionine, fad-dependent, oxidase, oxidoreductase |
| Biological source | Burkholderiales bacterium |
| Total number of polymer chains | 2 |
| Total formula weight | 113954.97 |
| Authors | |
| Primary citation | Kawamura, Y.,Sugiura, S.,Araseki, H.,Chisuga, T.,Nakano, S. Structural and functional analysis of l-methionine oxidase identified through sequence data mining. J.Biosci.Bioeng., 138:391-398, 2024 Cited by PubMed Abstract: l-Amino acid oxidase (LAAO), an FAD-dependent enzyme, catalyzes the oxidation of l-amino acids (l-AAs) to their corresponding imino acids. While LAAOs, which can oxidize charged or aromatic l-AAs specifically, have been extensively characterized across various species, LAAOs that have high specificity toward alkyl-chain l-AAs, such as l-Met, are hardly characterized for now. In this study, we screened a highly specific l-Met oxidizing LAAOs from Burkholderiales bacterium (BbMetOx) and Undibacterium sp. KW1 (UndMetOx) using sequence similarity network (SSN) analysis. These enzymes displayed an order of magnitude higher specific activity towards l-Met compared to other l-AAs. Enzyme activity assays showed that these LAAOs operate optimally at moderate condition because the optimal pH and T values were pH 7.0 and 58-60°C. We determined the crystal structures of wild-type BbMetOx (BbMetOx(WT)) and an inactivated mutant, BbMetOx (K304A), at 2.7 Å and 2.2 Å resolution, respectively. The overall structure of BbMetOx is closely similar to other known LAAOs of which structures were determined. Comparative analysis of the BbMetOx structures revealed significant conformational changes in the catalytic domain, particularly a movement of approximately 8 Å in the C atom of residue Y180. Further analysis highlighted four residues, i.e., Y180, M182, F300, and M302, as critical for l-Met recognition, with alanine substitution at these positions resulting in loss of activity. This study not only underscores the utility of SSN for discovering novel LAAOs but also advances our understanding of substrate specificity in this enzyme family. PubMed: 39142977DOI: 10.1016/j.jbiosc.2024.07.014 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.69 Å) |
Structure validation
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