8YNW

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

Summary for 8YNW

• Entry DOI: 10.2210/pdb8ynw/pdb
• Descriptor: Poly(3-hydroxybutyrate) depolymerase, 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (4 entities in total)
• Functional Keywords: mutant, depolymerase, hydrolase
• Biological source: Bacillus thuringiensis
• Total number of polymer chains: 4
• Total formula weight: 142956.29

Authors

Wang, Y.L.,Ye, L.C.,Chen, S.C.,Hsu, C.H. (deposition date: 2024-03-12, release date: 2024-12-11)

Primary citation

Wang, Y.L.,Ye, L.C.,Chang, S.C.,Chen, S.C.,Hsu, C.H.
Structural insight into the poly(3-hydroxybutyrate) hydrolysis by intracellular PHB depolymerase from Bacillus thuringiensis.
Int.J.Biol.Macromol., 284:137999-137999, 2024

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.

PubMed: 39592048
DOI: 10.1016/j.ijbiomac.2024.137999

Experimental method

X-RAY DIFFRACTION (1.9 Å)