8YQJ
Crystal structure of HylD1
Summary for 8YQJ
| Entry DOI | 10.2210/pdb8yqj/pdb |
| Descriptor | Lipase (2 entities in total) |
| Functional Keywords | phthalate ester hydrolase, dimer, wild-type, hydrolase |
| Biological source | Paracoccus kondratievae |
| Total number of polymer chains | 2 |
| Total formula weight | 62099.94 |
| Authors | |
| Primary citation | Wang, N.,Zhang, N.,Sun, M.L.,Sun, Y.,Dong, Q.Y.,Wang, Y.,Gu, Z.T.,Ding, H.T.,Qin, Q.L.,Jiang, Y.,Chen, X.L.,Zhang, Y.Z.,Gao, C.,Li, C.Y. Molecular insights into the catalytic mechanism of a phthalate ester hydrolase. J Hazard Mater, 476:135191-135191, 2024 Cited by PubMed Abstract: Phthalate esters (PAEs) are emerging hazardous and toxic chemicals that are extensively used as plasticizers or additives. Diethyl phthalate (DEP) and dimethyl phthalate (DMP), two kinds of PAEs, have been listed as the priority pollutants by many countries. PAE hydrolases are the most effective enzymes in PAE degradation, among which family IV esterases are predominate. However, only a few PAE hydrolases have been characterized, and as far as we know, no crystal structure of any PAE hydrolases of the family IV esterases is available to date. HylD1 is a PAE hydrolase of the family IV esterases, which can degrade DMP and DEP. Here, the recombinant HylD1 was characterized. HylD1 maintained a dimer in solution, and functioned under a relatively wide pH range. The crystal structures of HylD1 and its complex with monoethyl phthalate were solved. Residues involved in substrate binding were identified. The catalytic mechanism of HylD1 mediated by the catalytic triad Ser140-Asp231-His261 was further proposed. The hylD1 gene is widely distributed in different environments, suggesting its important role in PAEs degradation. This study provides a better understanding of PAEs hydrolysis, and lays out favorable bases for the rational design of highly-efficient PAEs degradation enzymes for industrial applications in future. PubMed: 39013318DOI: 10.1016/j.jhazmat.2024.135191 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.69 Å) |
Structure validation
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