9KNL | pdb_00009knl

Crystal structure of triethylene glycol-bound full-length PHA synthase (PhaC) from Aeromonas caviae

• PDB DOI: https://doi.org/10.2210/pdb9KNL/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Aeromonas caviae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-19 Released: 2025-05-21 
• Deposition Author(s): Chek, M.F., Kim, S.Y., Mori, T., Hakoshima, T.
• Funding Organization(s): New Energy and Industrial Technology Development Organization (NEDO), Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Structures of Polyhydroxyalkanoate Synthase PhaC from Aeromonas caviae, Producing Biodegradable Plastics.

Chek, M.F., Kim, S.Y., Mori, T., Matsumoto, K., Sato, S., Hakoshima, T.

(2025) Angew Chem Int Ed Engl 64: e202504626-e202504626

• PubMed: 40276819 
• DOI: https://doi.org/10.1002/anie.202504626
• Primary Citation of Related Structures:  
  9KNJ, 9KNK, 9KNL


• PubMed Abstract: 
  

  Polyhydroxyalkanoate (PHA) is a biodegradable polyester that can serve as a promising alternative to petrochemical plastics, which present a serious source of pollution. PHA synthase (PhaC) is a key enzyme responsible for producing a wide variety of PHAs in microorganisms. Here, we present crystal structures of full-length PhaC from Aeromonas caviae, a high-performance PhaC employed for industrial use. The structure reveals an N-terminal helical domain that mediates head-to-head dimerization and stabilizes the C-terminal α/β catalytic domain to form a tunnel that connects the catalytic center embedded inside the protein to the protein surface. We showed that this tunnel is a putative egress tunnel for the product PHA chain. Our results establish a fundamental understanding of the PhaC machinery that should lead to improvement of this enzyme in industrial applications.

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Organizational Affiliation: 
• Structural Biology and Protein Engineering Laboratory, Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.
Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.
Agri-Bio & Supplement Research Laboratories, Kaneka Corporation, 1-8 Miyamae-cho, Takasago-cho, Takasago, Hyogo, 676-8688, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: equilibrium centrifugation, gel filtration

Macromolecule Content 

• Total Structure Weight: 199.96 kDa 
• Atom Count: 12,399 
• Modeled Residue Count: 1,564 
• Deposited Residue Count: 1,788 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHA synthase	A, B, C	596	Aeromonas caviae	Mutation(s): 0  Gene Names: phaC
UniProt
Find proteins for O32471 (Aeromonas caviae) Explore O32471  Go to UniProtKB:  O32471

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE (Subject of Investigation/LOI)	D [auth A], E [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.247 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.713	α = 90
b = 95.53	β = 90.7
c = 141.174	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-21 
Deposition Author(s): Chek, M.F., Kim, S.Y., Mori, T., Hakoshima, T.

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Funding Organization	Location	Grant Number
New Energy and Industrial Technology Development Organization (NEDO)	Japan	P20005
Japan Science and Technology	Japan	29A1027
Japan Society for the Promotion of Science (JSPS)	Japan	21K15028

Revision History  

• Version 1.0: 2025-05-21
  Type: Initial release
  
• Version 1.1: 2025-07-09
  Changes: Database references