8DAJ | pdb_00008daj

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 (Depositor), 0.177 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

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 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.

Macromolecule Content 

  • Total Structure Weight: 33.3 kDa 
  • Atom Count: 2,779 
  • Modeled Residue Count: 302 
  • Deposited Residue Count: 302 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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 (Depositor), 0.177 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
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

View Full Validation Report



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
  • Version 1.1: 2024-10-23
    Changes: Data collection, Structure summary