5T6O

Structure of the catalytic domain of the class I polyhydroxybutyrate synthase from Cupriavidus necator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the Catalytic Domain of the Class I Polyhydroxybutyrate Synthase from Cupriavidus necator.

Wittenborn, E.C.Jost, M.Wei, Y.Stubbe, J.Drennan, C.L.

(2016) J.Biol.Chem. 291: 25264-25277

  • DOI: 10.1074/jbc.M116.756833

  • PubMed Abstract: 
  • Polyhydroxybutyrate synthase (PhaC) catalyzes the polymerization of 3-(R)-hydroxybutyryl-coenzyme A as a means of carbon storage in many bacteria. The resulting polymers can be used to make biodegradable materials with properties similar to those of ...

    Polyhydroxybutyrate synthase (PhaC) catalyzes the polymerization of 3-(R)-hydroxybutyryl-coenzyme A as a means of carbon storage in many bacteria. The resulting polymers can be used to make biodegradable materials with properties similar to those of thermoplastics and are an environmentally friendly alternative to traditional petroleum-based plastics. A full biochemical and mechanistic understanding of this process has been hindered in part by a lack of structural information on PhaC. Here we present the first structure of the catalytic domain (residues 201-589) of the class I PhaC from Cupriavidus necator (formerly Ralstonia eutropha) to 1.80 Å resolution. We observe a symmetrical dimeric architecture in which the active site of each monomer is separated from the other by ∼33 Å across an extensive dimer interface, suggesting a mechanism in which polyhydroxybutyrate biosynthesis occurs at a single active site. The structure additionally highlights key side chain interactions within the active site that play likely roles in facilitating catalysis, leading to the proposal of a modified mechanistic scheme involving two distinct roles for the active site histidine. We also identify putative substrate entrance and product egress routes within the enzyme, which are discussed in the context of previously reported biochemical observations. Our structure lays a foundation for further biochemical and structural characterization of PhaC, which could assist in engineering efforts for the production of eco-friendly materials.


    Organizational Affiliation

    From the Departments of Chemistry.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly-beta-hydroxybuterate polymerase
A
389Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)Gene Names: phbC
EC: 2.3.1.-
Find proteins for P23608 (Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337))
Go to UniProtKB:  P23608
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 72.080α = 90.00
b = 87.820β = 90.00
c = 137.100γ = 90.00
Software Package:
Software NamePurpose
SHELXDEphasing
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM069857
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32 GM008334

Revision History 

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-02
    Type: Database references
  • Version 1.2: 2016-12-07
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Database references