8Z59

The X-Ray crystal structure of multicopper oxidase from Sulfurimonas sp.

Summary for 8Z59

• Entry DOI: 10.2210/pdb8z59/pdb
• Descriptor: Bilirubin oxidase, COPPER (II) ION (3 entities in total)
• Functional Keywords: oxidation, polyphenol, oxidoreductase
• Biological source: Sulfurimonas sp.
• Total number of polymer chains: 8
• Total formula weight: 468116.72

Authors

Wang, Y.,Qian, H. (deposition date: 2024-04-18, release date: 2025-02-19, Last modification date: 2025-09-03)

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

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: 40188191
DOI: 10.1038/s41467-025-58521-y

Experimental method

X-RAY DIFFRACTION (2.58 Å)