9U9U | pdb_00009u9u

Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Lys181Lys/Trp185Tyr/His280Ala with (S)-2-fluoro-3-(4-(trifluoromethyl)phenyl)propanoic acid

• PDB DOI: https://doi.org/10.2210/pdb9U9U/pdb

• Classification: TRANSFERASE
• Organism(s): Rhodopseudomonas palustris CGA009
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-03-29 Released: 2025-12-31 
• Deposition Author(s): Huang, H.S., Zhang, Z.M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.254 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Creating highly active fluoroacetate dehalogenases via gate-based synergetic chain design.

Wang, C.Z., Huang, H., Hu, Z., Gao, L., Lin, Z.Q., Shi, M., Song, Z., Li, M., Wang, Y., Chen, K.W., Liu, Y., Ma, Y., Chen, B., Yan, Q., Zhang, Z.M., Wang, J.B.

(2026) Nat Commun 17

• PubMed: 42062289 
• DOI: https://doi.org/10.1038/s41467-026-72741-w
• Primary Citation Related Structures: 
  21BK, 9U5W, 9U5X, 9U9L, 9U9U, 9UE2


• PubMed Abstract: 
  

  Gate residues, acting in concert with distal dynamic networks, are emerging as critical yet underexploited regulators of enzymatic catalysis. Here we show that conformational dynamics analysis of fluoroacetate dehalogenase RPA1163 reveals a gate-based allosteric pair (K181-W185) that governs substrate access and reactivity. Network engineering of this pair yields a double mutant with high turnover number for α-fluorophenylpropionic acid (turnover number > 2 × 10⁵), establishing gate-centric allostery as a generalizable design principle. Structural and molecular dynamics analyses show that the activity enhancement arises from stabilization of catalytically competent open states through long-range coupling. Extension of this strategy to three additional dehalogenases confirms the universality of gate-based dynamic rewiring. Leveraging this framework, we establish a robust biocatalytic platform for stereoselective synthesis of α-fluoro and α-hydroxy carboxylic acids, achieving high productivity (turnover number > 3.7 × 10⁶) and enabling decagram-scale preparation of pharmaceutically relevant intermediates with high yield and enantioselectivity. Together, these findings establish gate-residue allostery as a powerful concept in protein engineering, bridging conformational dynamics with translational biocatalysis.

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Organizational Affiliation: 
• Key Laboratory of Multiple Organ Failure (Zhejiang University), Ministry of Education, Department of General Intensive Care Unit of the Second Affiliated Hospital (Zhejiang University), Zhejiang University School of Medicine, Hangzhou, P. R. China.
Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education) and Key Laboratory of Phytochemistry R&D of Hunan Province, College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha, P. R. China.
Guangxi Key Laboratory of Urban Water Environment, College of Chemistry and Environmental Engineering, Baise University, Baise, P. R. China.
State Key Laboratory of Bioactive Molecules and Druggability Assessment, Pharmacy College, Jinan University, Guangzhou, P. R. China.
Key Laboratory of Tea Science of Ministry of Education, College of Horticulture, Hunan Agricultural University, Changsha, P. R. China.
Lab of Computational Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, P. R. China.
College of Life Sciences, Zhejiang University, Hangzhou, P. R. China.
Hunan Provincial Key Laboratory of Animal Models and Molecular Medicine, School of Biomedical Sciences, Hunan University, Changsha, Hunan, P. R. China. [e-mail].
Greater Bay Area Institute for Innovation, Hunan University, Guangzhou, Guangdong, P. R. China. [e-mail].
State Key Laboratory of Bioactive Molecules and Druggability Assessment, Pharmacy College, Jinan University, Guangzhou, P. R. China. [e-mail].
Key Laboratory of Multiple Organ Failure (Zhejiang University), Ministry of Education, Department of General Intensive Care Unit of the Second Affiliated Hospital (Zhejiang University), Zhejiang University School of Medicine, Hangzhou, P. R. China. [e-mail].
Department of Microbiology, Zhejiang University School of Medicine, Hangzhou, Guangdong, P. R. China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 135.46 kDa 
• Atom Count: 9,622 
• Modeled Residue Count: 1,192 
• Deposited Residue Count: 1,208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fluoroacetate dehalogenase	A, B, C, D	302	Rhodopseudomonas palustris CGA009	Mutation(s): 3  Gene Names: RPA1163 EC: 3.8.1.3
UniProt
Find proteins for Q6NAM1 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NAM1  Go to UniProtKB:  Q6NAM1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1ES3 (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	3-[4-(trifluoromethyl)phenyl]propanoic acid C10 H9 F3 O2 OEIUMLSCWINLBB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.254 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.698	α = 90
b = 86.952	β = 109.276
c = 86.02	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Huang, H.S., Zhang, Z.M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release
  
• Version 1.1: 2026-07-15
  Changes: Database references