9LF7 | pdb_00009lf7

A PAE-hydrolyse Poc14


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.178 (Depositor), 0.179 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.154 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Molecular Insight Into the Hydrolysis of Phthalate Esters by a Family IV Esterase.

Rong, Z.Hong, L.G.Huo, Y.Y.Li, J.Zheng, D.Q.Ha, Y.Fan, J.Xu, X.W.Wu, Y.H.

(2025) Environ Microbiol 27: e70134-e70134

  • DOI: https://doi.org/10.1111/1462-2920.70134
  • Primary Citation of Related Structures:  
    9LF7

  • PubMed Abstract: 

    Phthalate esters (PAEs) are prevalent environmental contaminants, with their biodegradation efficiently driven by microorganisms through ester bond hydrolysis. This study investigates the mechanism of Poc14, a novel family IV esterase, using x-ray crystallography, bioinformatics, biochemistry and site-directed mutagenesis. Phylogenetic analysis classifies Poc14 as a family IV esterase with conserved catalytic motifs crucial for its activity. Poc14 retains over 80% activity at 50°C for 4 h and tolerates up to 5% methanol or DMF, though surfactants like Tweens inhibit its function. Poc14 activity is independent of metal ions, and the addition of EDTA further enhances its activity by approximately 130%. The 1.8 Å crystal structure reveals a CAP domain and two substrate channels. Enzyme assays show Poc14 hydrolyses short-chain diethyl phthalate (DEP) (K m  = 0.068 mM, V max  = 9975 μM/min/mg) but not long-chain di(2-ethylhexyl) phthalate (DEHP) due to steric hindrance. Molecular docking assessed Poc14's potential to hydrolyse DEP and DEHP after residue mutations, resulting in the Poc14-AAG variant. Poc14-AAG could hydrolyse one bond of DEHP and diester bonds of DEP. Our study positions Poc14 as a promising enzyme for environmental remediation, with potential for optimising DEHP degradation and exploring dimerisation effects.


  • Organizational Affiliation
    • State Key Laboratory of Submarine Geoscience, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, People's Republic of China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poc14_A
A, B
336Erythrobacter cryptus DSM 12079Mutation(s): 0 
Gene Names: poc14
EC: 3.1.1.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.178 (Depositor), 0.179 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.154 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.657α = 90
b = 89.603β = 90
c = 139.592γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChina--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Database references