8WM1 | pdb_00008wm1

DHS dehydratase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 
    0.255 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.224 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Efficient production of protocatechuic acid using systems engineering of Escherichia coli.

Wang, M.Wang, H.Gao, C.Wei, W.Liu, J.Chen, X.Hu, G.Song, W.Wu, J.Zhang, F.Liu, L.

(2024) Metab Eng 82: 134-146

  • DOI: https://doi.org/10.1016/j.ymben.2024.02.003
  • Primary Citation of Related Structures:  
    8WM1

  • PubMed Abstract: 

    Protocatechuic acid (3, 4-dihydroxybenzoic acid, PCA) is widely used in the pharmaceuticals, health food, and cosmetics industries owing to its diverse biological activities. However, the inhibition of 3-dehydroshikimate dehydratase (AroZ) by PCA and its toxicity to cells limit the efficient production of PCA in Escherichia coli. In this study, a high-level strain of 3-dehydroshikimate, E. coli DHS01, was developed by blocking the carbon flow from the shikimate-overproducing strain E. coli SA09. Additionally, the PCA biosynthetic pathway was established in DHS01 by introducing the high-activity ApAroZ. Subsequently, the protein structure and catalytic mechanism of 3-dehydroshikimate dehydratase from Acinetobacter pittii PHEA-2 (ApAroZ) were clarified. The variant ApAroZ R363A , achieved by modulating the conformational dynamics of ApAroZ, effectively relieved product inhibition. Additionally, the tolerance of the strain E. coli PCA04 to PCA was enhanced by adaptive laboratory evolution, and a biosensor-assisted high-throughput screening method was designed and implemented to expedite the identification of high-performance PCA-producing strains. Finally, in a 5 L bioreactor, the final strain PCA05 achieved the highest PCA titer of 46.65 g/L, a yield of 0.23 g/g, and a productivity of 1.46 g/L/h for PCA synthesis from glucose using normal fed-batch fermentation. The strategies described herein serve as valuable guidelines for the production of other high-value and toxic products.


  • Organizational Affiliation
    • School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, 214122, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-dehydroshikimate dehydratase (DHS dehydratase)
A, B, C, D
484Acinetobacter pittii PHEA-2Mutation(s): 0 
Gene Names: quiC
UniProt
Find proteins for F0KF79 (Acinetobacter pittii (strain PHEA-2))
Explore F0KF79 
Go to UniProtKB:  F0KF79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF0KF79
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free:  0.255 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.224 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.56α = 90
b = 97.67β = 90
c = 132.82γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2024-10-02 
  • Deposition Author(s): Wang, M.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Structure summary
  • Version 1.2: 2025-04-16
    Changes: Database references