5T6O

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

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This is version 1.4 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
  • Primary Citation of Related Structures:  
    5T6O

  • 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 thermoplastics and are an environmentally friendly alternative to traditional petroleum-based plastics ...

    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

    Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly-beta-hydroxybuterate polymeraseA389Cupriavidus necatorMutation(s): 1 
Gene Names: 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.08α = 90
b = 87.82β = 90
c = 137.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM069857
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM008334

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2016-11-02
    Changes: Database references
  • Version 1.2: 2016-12-07
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Database references
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence