8DAJ

Structure and Biochemistry of a Promiscuous Thermophilic Polyhydroxybutyrate Depolymerase from Lihuaxuella thermophilia


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

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Ligand Structure Quality Assessment 


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Literature

Bioplastic degradation by a polyhydroxybutyrate depolymerase from a thermophilic soil bacterium.

Thomas, G.M.Quirk, S.Huard, D.J.E.Lieberman, R.L.

(2022) Protein Sci 31: e4470-e4470

  • DOI: https://doi.org/10.1002/pro.4470
  • Primary Citation of Related Structures:  
    8DAJ

  • PubMed Abstract: 

    As the epidemic of single-use plastic worsens, it has become critical to identify fully renewable plastics such as those that can be degraded using enzymes. Here we describe the structure and biochemistry of an alkaline poly[(R)-3-hydroxybutyric acid] (PHB) depolymerase from the soil thermophile Lihuaxuella thermophila. Like other PHB depolymerases or PHBases, the Lihuaxuella enzyme is active against several different polyhydroxyalkanoates, including homo- and heteropolymers, but L. thermophila PHB depolymerase (LtPHBase) is unique in that it also hydrolyzes polylactic acid and polycaprolactone. LtPHBase exhibits optimal activity at 70°C, and retains 88% of activity upon incubation at 65°C for 3 days. The 1.2 Å resolution crystal structure reveals an α/β-hydrolase fold typical of PHBases, but with a shallow active site containing the catalytic Ser-His-Asp-triad that appears poised for broad substrate specificity. LtPHBase holds promise for the depolymerization of PHB and related bioplastics at high temperature, as would be required in bioindustrial operations like recycling or landfill management.


  • Organizational Affiliation

    School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Esterase, PHB depolymerase family302Lihuaxuella thermophilaMutation(s): 0 
Gene Names: SAMN05444955_11823
UniProt
Find proteins for A0A1H8IKU3 (Lihuaxuella thermophila)
Explore A0A1H8IKU3 
Go to UniProtKB:  A0A1H8IKU3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1H8IKU3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO (Subject of Investigation/LOI)
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
H [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
H [auth A],
J [auth A],
K [auth A],
L [auth A],
N [auth A],
O [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA (Subject of Investigation/LOI)
Query on IPA

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
I [auth A],
M [auth A]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.51α = 90
b = 45.51β = 90
c = 211.26γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1817796

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-15
    Type: Initial release