Crystal structure analysis, covalent docking, and molecular dynamics calculations reveal a conformational switch in...

Area of Science:

• Enzymology
• Structural Biology
• Biochemistry

Background:

• Poly(3-hydroxybutyrate) depolymerases (PhaZs) are enzymes crucial for degrading PHB bioplastics.
• Understanding the structure-function relationship of PhaZs, like PhaZ7, is key to optimizing their industrial applications.

Purpose of the Study:

• To investigate the conformational dynamics of a surface loop in PhaZ7 extracellular poly(3-hydroxybutyrate) depolymerase.
• To elucidate the role of this flexible loop in substrate binding and enzyme activity.

Main Methods:

• High-resolution crystal structures of a PhaZ7 Y105E mutant.
• Molecular dynamics (MD) simulations.
• Covalent docking of a 3-hydroxybutyric acid trimer.

Main Results:

• Two conformations (open and closed) of the 281-295 surface loop were identified.
• The loop exhibited high root mean square fluctuations (RMSF), particularly at Asp289.
• Substrate binding energy was more favorable in the open loop conformation.
• Substrate presence enhanced the loop's ability to adopt a closed form.

Conclusions:

• The flexible loop 281-295 functions as a lid domain, regulating substrate access to the PhaZ7 active site.
• Enzyme dynamics and substrate interaction are critical for controlling enzymatic activity.