8Z5B
The X-Ray crystal structure of multicopper oxidase from Bacillus freudenreichii
Summary for 8Z5B
| Entry DOI | 10.2210/pdb8z5b/pdb |
| Descriptor | Multicopper oxidase, MANGANESE (II) ION, COPPER (II) ION, ... (4 entities in total) |
| Functional Keywords | oxidized polyphenol substrates, oxidoreductase |
| Biological source | Bacillus freudenreichii |
| Total number of polymer chains | 1 |
| Total formula weight | 63833.76 |
| Authors | |
| Primary citation | Qian, H.,Wang, Y.,Zhou, X.,Gu, T.,Wang, H.,Lyu, H.,Li, Z.,Li, X.,Zhou, H.,Guo, C.,Yuan, F.,Wang, Y. ESM-Ezy: a deep learning strategy for the mining of novel multicopper oxidases with superior properties. Nat Commun, 16:3274-3274, 2025 Cited by PubMed Abstract: The UniProt database is a valuable resource for biocatalyst discovery, yet predicting enzymatic functions remains challenging, especially for low-similarity sequences. Identifying superior enzymes with enhanced catalytic properties is even harder. To overcome these challenges, we develop ESM-Ezy, an enzyme mining strategy leveraging the ESM-1b protein language model and similarity calculations in semantic space. Using ESM-Ezy, we identify novel multicopper oxidases (MCOs) with superior catalytic properties, achieving a 44% success rate in outperforming query enzymes (QEs) in at least one property, including catalytic efficiency, heat and organic solvent tolerance, and pH stability. Notably, 51% of the MCOs excel in environmental remediation applications, and some exhibited unique structural motifs and unique active centers enhancing their functions. Beyond MCOs, 40% of L-asparaginases identified show higher specific activity and catalytic efficiency than QEs. ESM-Ezy thus provides a promising approach for discovering high-performance biocatalysts with low sequence similarity, accelerating enzyme discovery for industrial applications. PubMed: 40188191DOI: 10.1038/s41467-025-58521-y PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.4 Å) |
Structure validation
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