8J5V | pdb_00008j5v

Crystal structure of estZF172 as a novel biocatalyst for the efficient biosynthesis of a chiral intermediate of pregabalin

• PDB DOI: https://doi.org/10.2210/pdb8J5V/pdb

• Classification: LYASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-24 Released: 2024-05-01 
• Deposition Author(s): Chi, C.B., Liang, Z.D., Huo, B.Q., Hu, C.X., Sun, Q.Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.236 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of EstZF172 Catalyzing Stereoselectively ( R )‐CNDE in Pregabalin Biosynthesis.

Liang, Z., Ma, X., Sun, Q., Zhang, X., Wang, G., Chi, C.

(2025) ACS Omega 10: 21693-21700

• PubMed: 40488026 
• DOI: https://doi.org/10.1021/acsomega.5c01054
• Primary Citation of Related Structures:  
  8J5V


• PubMed Abstract: 
  

  Pregabalin has garnered extensive clinical application for the management of neuropathic pain and epilepsy owing to its high efficacy and broad drug concentration range. EstZF172 is a key enzyme in the biosynthesis of pregabalin, capable of stereoselectively catalyzing the production of ( R )-CCMA from the key intermediate rac -CNDE. The novel crystal structure of EstZF172 indicates that it contains a highly conserved Ser-Lys-Tyr catalytic triad and belongs to the family VIII ₂ carboxylesterases. Molecular docking demonstrates that the steric hindrance presented by residues I159 and F239 plays a crucial role in influencing the binding affinity of the chiral substrate ( R )-CNDE for the catalytic site. The study provides a structural basis and reference for the stereoselective catalysis of EstZF172 and engineering modification of the key enzyme in the synthesis of pregabalin.

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Organizational Affiliation: 
• Department of Bioengineering and Biotechnology, Huaqiao University, Jimei Ave. 668, Xiamen 361021, China.
Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193 China.
Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 44.06 kDa 
• Atom Count: 2,848 
• Modeled Residue Count: 361 
• Deposited Residue Count: 404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carboxylesterase	A	404	Pseudomonas putida	Mutation(s): 0  Gene Names: estC, WP8W18C01_39630
UniProt
Find proteins for A0A6S5TYM3 (Pseudomonas putida) Explore A0A6S5TYM3  Go to UniProtKB:  A0A6S5TYM3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.236 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.378	α = 90
b = 85.667	β = 90
c = 89.854	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-01 
Deposition Author(s): Chi, C.B., Liang, Z.D., Huo, B.Q., Hu, C.X., Sun, Q.Y.

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Funding Organization	Location	Grant Number
Not funded	China	--

Revision History  

• Version 1.0: 2024-05-01
  Type: Initial release
  
• Version 1.1: 2025-12-10
  Changes: Database references, Structure summary