8YQJ image
Deposition Date 2024-03-19
Release Date 2024-07-31
Last Version Date 2024-07-31
Entry Detail
PDB ID:
8YQJ
Keywords:
Title:
Crystal structure of HylD1
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
1.69 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Lipase
Chain IDs:A, B
Chain Length:291
Number of Molecules:2
Biological Source:Paracoccus kondratievae
Primary Citation
Molecular insights into the catalytic mechanism of a phthalate ester hydrolase.
J Hazard Mater 476 135191 135191 (2024)
PMID: 39013318 DOI: 10.1016/j.jhazmat.2024.135191

Abstact

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.

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