8YNW | pdb_00008ynw

S102A mutant of poly(3-hydroxybutyrate) depolymerase PhaZ from Bacillus thuringiensis

• PDB DOI: https://doi.org/10.2210/pdb8YNW/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus thuringiensis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-03-12 Released: 2024-12-11 
• Deposition Author(s): Wang, Y.L., Ye, L.C., Chen, S.C., Hsu, C.H.
• Funding Organization(s): National Science Council (NSC, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Structural insight into the poly(3-hydroxybutyrate) hydrolysis by intracellular PHB depolymerase from Bacillus thuringiensis.

Wang, Y.L., Ye, L.C., Chang, S.C., Chen, S.C., Hsu, C.H.

(2024) Int J Biol Macromol 284: 137999-137999

• PubMed: 39592048 
• DOI: https://doi.org/10.1016/j.ijbiomac.2024.137999
• Primary Citation of Related Structures:  
  8YNV, 8YNW


• PubMed Abstract: 
  

  Poly((R)-3-hydroxybutyrate) (PHB) is a microbial biopolymer widely used in commercial biodegradable plastics. PHB degradation in cell is catalyzed by PHB depolymerase (PhaZ), which hydrolyzes the polyester into mono- and/or oligomeric (R)-3-hydroxylbutyrates (3HB). A novel intracellular PhaZ from Bacillus thuringiensis (BtPhaZ) was identified for potential applications in polymer biodegradation and 3HB production. Herein, we present the crystal structure of BtPhaZ at 1.42-Å resolution, making the first crystal structure for an intracellular PhaZ. BtPhaZ comprises a canonical α/β hydrolase catalytic domain and a unique α-helical cap domain. Despite lacking sequence similarity, BtPhaZ shares high structural homology with many α/β hydrolase members, exhibiting a similar active-site architecture. Alongside the most conserved superfamily signature, several new conserved signatures have been identified, contributing not only to the formations of the Ser-His-Asp catalytic triad and the oxyanion hole but also to the active-site conformation. The putative P-1 subsite appears to have limited space for accommodating only one 3HB-monomer, which may provide an explanation why the major hydrolytic product for BtPhaZ is monomeric form. Furthermore, a cluster of solvent-exposed hydrophobic residues in the helical cap domain forms an adsorption site for polymer-binding. Detailed structural comparisons reveal that various PhaZs employ distinct residues for the biopolymer-binding and hydrolysis.

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Organizational Affiliation: 
• Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan.
Department of Seafood Science, National Kaohsiung University of Science and Technology, No. 142, Haijhuan Rd, Nanzih District, Kaohsiung 81157, Taiwan. Electronic address: [e-mail].
Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan; Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan; Center for Computational and Systems Biology, National Taiwan University, Taipei 10617, Taiwan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: equilibrium centrifugation

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 142.96 kDa 
• Atom Count: 10,562 
• Modeled Residue Count: 1,189 
• Deposited Residue Count: 1,244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(3-hydroxybutyrate) depolymerase	A, B, C, D	311	Bacillus thuringiensis	Mutation(s): 1  Gene Names: BK719_31655
UniProt
Find proteins for A0A9W3JUC0 (Bacillus thuringiensis HD-789) Explore A0A9W3JUC0  Go to UniProtKB:  A0A9W3JUC0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P33 (Subject of Investigation/LOI)	E [auth B], F [auth D]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
TRS (Subject of Investigation/LOI)	G [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.989	α = 73.484
b = 83.552	β = 82.839
c = 85.729	γ = 83.617

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-11 
Deposition Author(s): Wang, Y.L., Ye, L.C., Chen, S.C., Hsu, C.H.

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Funding Organization	Location	Grant Number
National Science Council (NSC, Taiwan)	Taiwan	111-2113-M-002-015-MY3

Revision History  

• Version 1.0: 2024-12-11
  Type: Initial release