9KNJ | pdb_00009knj

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

PDB DOI: https://doi.org/10.2210/pdb9KNJ/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.249 (Depositor), 0.249 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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 Search on PubMed
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.

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.

Macromolecule Content

Total Structure Weight: 200.68 kDa
Atom Count: 12,874
Modeled Residue Count: 1,617
Deposited Residue Count: 1,788
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O32471
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain E [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth C], N [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.249 (Depositor), 0.249 (DCC)
R-Value Work: 0.210 (Depositor), 0.210 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.032	α = 90
b = 96.071	β = 90.42
c = 143.296	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

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	21K5028