6K3C | pdb_00006k3c

Crystal structure of class I PHA synthase (PhaC) mutant from Chromobacterium sp. USM2 bound to Coenzyme A.

• PDB DOI: https://doi.org/10.2210/pdb6K3C/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Chromobacterium sp. USM2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-05-17 Released: 2020-04-29 
• Deposition Author(s): Chek, M.F., Kim, S.Y., Mori, T., Hakoshima, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.07 Å
• R-Value Free: 
  0.263 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Asymmetric Open-Closed Dimer Mechanism of Polyhydroxyalkanoate Synthase PhaC.

Chek, M.F., Kim, S.Y., Mori, T., Tan, H.T., Sudesh, K., Hakoshima, T.

(2020) iScience 23: 101084-101084

• PubMed: 32388399 
• DOI: https://doi.org/10.1016/j.isci.2020.101084
• Primary Citation Related Structures: 
  6K3C


• PubMed Abstract: 
  

  Biodegradable polyester polyhydroxyalkanoate (PHA) is a promising bioplastic material for industrial use as a replacement for petroleum-based plastics. PHA synthase PhaC forms an active dimer to polymerize acyl moieties from the substrate acyl-coenzyme A (CoA) into PHA polymers. Here we present the crystal structure of the catalytic domain of PhaC from Chromobacterium sp. USM2, bound to CoA. The structure reveals an asymmetric dimer, in which one protomer adopts an open conformation bound to CoA, whereas the other adopts a closed conformation in a CoA-free form. The open conformation is stabilized by the asymmetric dimerization and enables PhaC to accommodate CoA and also to create the product egress path. The bound CoA molecule has its β-mercaptoethanolamine moiety extended into the active site with the terminal SH group close to active center Cys291, enabling formation of the reaction intermediate by acylation of Cys291.

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Organizational Affiliation: 
• Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia.
Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 88.42 kDa 
• Atom Count: 5,908 
• Modeled Residue Count: 739 
• Deposited Residue Count: 790 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intracellular polyhydroxyalkanoate synthase	A, B	395	Chromobacterium sp. USM2	Mutation(s): 1  Gene Names: phaC
UniProt
Find proteins for E1APK1 (Chromobacterium sp. USM2) Explore E1APK1  Go to UniProtKB:  E1APK1

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.07 Å
• R-Value Free:  0.263 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.802	α = 90
b = 61.852	β = 106.73
c = 82.566	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Chek, M.F., Kim, S.Y., Mori, T., Hakoshima, T.

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2020-05-27
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description