9BWL | pdb_00009bwl

Crystal structure of polyketoacyl-CoA thiolase from Burkholderia sp in complex with butyryl-coA

• PDB DOI: https://doi.org/10.2210/pdb9BWL/pdb

• Classification: LYASE
• Organism(s): Burkholderia sp. RF2-non_BP3
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-21 Released: 2025-08-27 
• Deposition Author(s): Pereira, J.H., Wang, Z., Keasling, J.D., Adams, P.D.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

A highly active Burkholderia polyketoacyl-CoA thiolase for production of triacetic acid lactone.

Wang, Z., Cheong, S., Pereira, J.H., Hu, W., Guo, Y., DeGiovanni, A., Lan, G., Kim, J., Haushalter, R.W., Lee, T.S., Adams, P.D., Keasling, J.D.

(2025) Nat Commun 16: 10990-10990

• PubMed: 41365852 
• DOI: https://doi.org/10.1038/s41467-025-65946-y
• Primary Citation of Related Structures:  
  9BWK, 9BWL, 9BWO, 9BWP


• PubMed Abstract: 
  

  Triacetic acid lactone (TAL) is a versatile platform chemical traditionally biosynthesized via decarboxylative Claisen condensation by 2-pyrone synthase. However, this route is limited by poor efficiency and dependence on malonyl-CoA. Here, we show that non-decarboxylative Claisen condensation by polyketoacyl-CoA thiolases offers a more efficient alternative. Through mining homologs of a previously reported enzyme from Cupriavidus necator, we identify five thiolases with TAL production activity. One candidate, BktBbr from Burkholderia sp. RF2-non_BP3, exhibits approximately 30-fold higher activity in vitro and supports 30-fold higher TAL titers in Escherichia coli compared to the original enzyme. Fed-batch fermentation achieves titers up to 2.8 g L⁻¹. Structural analysis of BktBbr co-crystallized with CoA esters guides rational engineering to further enhance performance. Our discovery of a highly active thiolase establishes an alternative enzymatic route to produce TAL efficiently, providing a scalable foundation for sustainable biomanufacturing.

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Organizational Affiliation: 
• Joint BioEnergy Institute, Emeryville, CA, USA.
Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA.
QB3 Institute, University of California, Berkeley, CA, USA.
Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
Joint BioEnergy Institute, Emeryville, CA, USA. [e-mail].
Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA. [e-mail].
Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [e-mail].
Center for Biosustainability, Danish Technical University, Lyngby, Denmark. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 84.42 kDa 
• Atom Count: 6,151 
• Modeled Residue Count: 787 
• Deposited Residue Count: 798 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-CoA acetyltransferase	A, B	399	Burkholderia sp. RF2-non_BP3	Mutation(s): 0  Gene Names: WS45_00950

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA (Subject of Investigation/LOI)	C [auth A], D [auth B]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CY4	A, B	L-PEPTIDE LINKING	C7 H13 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.325	α = 90
b = 130.325	β = 90
c = 120.703	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-27 
Deposition Author(s): Pereira, J.H., Wang, Z., Keasling, J.D., Adams, P.D.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--

Revision History  

• Version 1.0: 2025-08-27
  Type: Initial release
  
• Version 1.1: 2025-12-24
  Changes: Database references