Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 44.51 kDa 
• Atom Count: 3340 
• Modelled Residue Count: 388 
• Deposited Residue Count: 396 
• Unique protein chains: 1

5HZ2

Crystal structure of PhaC1 from Ralstonia eutropha

• PDB DOI: 10.2210/pdb5HZ2/pdb

• Classification: TRANSFERASE
• Organism(s): Cupriavidus necator H16
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-02 Released: 2016-12-07 
• Deposition Author(s): Kim, J., Kim, K.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.190 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 

Literature

Crystal structure of Ralstonia eutropha polyhydroxyalkanoate synthase C-terminal domain and reaction mechanisms.

Kim, J., Kim, Y.J., Choi, S.Y., Lee, S.Y., Kim, K.J.

(2017) Biotechnol J 12

• PubMed: 27808482 
• DOI: 10.1002/biot.201600648
• Primary Citation of Related Structures:  
  5HZ2


• PubMed Abstract: 
  

Polyhydroxyalkanoates (PHAs) are natural polyesters synthesized by numerous microorganisms as energy and reducing power storage materials, and have attracted much attention as substitutes for petroleum-based plastics. Here, we report the first crystal structure of Ralstonia eutropha PHA synthase at 1.8 Å resolution and structure-based mechanisms for PHA polymerization. RePhaC1 contains two distinct domains, the N-terminal (RePhaC1 _ND ) and C-terminal domains (RePhaC1 _CD ), and exists as a dimer. RePhaC1 _CD catalyzes polymerization via non-processive ping-pong mechanism using a Cys-His-Asp catalytic triad. Molecular docking simulation of 3-hydroxybutyryl-CoA to the active site of RePhaC1 _CD reveals residues involved in the formation of 3-hydroxybutyryl-CoA binding pocket and substrate binding tunnel. Comparative analysis with other polymerases elucidates how different classes of PHA synthases show different substrate specificities. Furthermore, we attempted structure-based protein engineering and developed a RePhaC1 mutant with enhanced PHA synthase activity.

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Organizational Affiliation: 

School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly-beta-hydroxybutyrate polymerase	A	396	Cupriavidus necator H16	Mutation(s): 0  Gene Names: phbC, H16_A1437, phaC EC: 2.3.1
UniProt
Find proteins for P23608 (Cupriavidus necator (strain ATCC 17699 / DSM 428 / KCTC 22496 / NCIMB 10442 / H16 / Stanier 337)) Explore P23608  Go to UniProtKB:  P23608

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A], C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.190 
• R-Value Work: 0.151 
• R-Value Observed: 0.153 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.246	α = 90
b = 87.856	β = 90
c = 136.479	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-02-02 
• Released Date: 2016-12-07 
Deposition Author(s): Kim, J., Kim, K.-J.

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2017-04-05
  Changes: Database references