The modular structure of α/β-hydrolases

Area of Science:

• Biochemistry and Molecular Biology
• Enzymology
• Structural Biology

Background:

• The alpha/beta-hydrolase fold family is characterized by significant diversity in sequence, structure, and biochemical function.
• Understanding the intricate sequence-structure-function relationships within this family is crucial for protein engineering and biocatalysis.

Purpose of the Study:

• To update and analyze the Lipase Engineering Database (LED) for comprehensive insights into alpha/beta-hydrolase diversity.
• To establish a classification system for alpha/beta-hydrolases based on their structural architectures and conserved sequence motifs.
• To investigate the evolutionary relationships and network properties within the alpha/beta-hydrolase superfamily.

Main Methods:

• Analysis of 280,638 protein sequences and 1,557 protein structures from the updated Lipase Engineering Database.
• Development of a classification system based on core domains, additional structural modules (lids, caps, N-/C-terminal domains), and oxyanion hole signatures (GX-, GGGX-, Y-types).
• Investigation of evolutionary relationships using sequence network analysis, including degree distribution and cluster size distribution.

Main Results:

• Identification of 12 distinct architectural types for alpha/beta-hydrolases, incorporating variations in core domains and accessory modules.
• Characterization of N-terminal domains (Rossmann or beta-propeller fold) and C-terminal domains (beta-sandwich fold), noting structural similarities to carbohydrate-binding proteins.
• Classification of newly discovered polyethylene terephthalate (PET)-degrading enzymes (PETases and MHETases) within the established framework.
• Analysis revealed a highly inhomogeneous evolutionary network for alpha/beta-hydrolases, following power-law distributions indicative of a robust, interconnected sequence space.

Conclusions:

• The established classification system provides a robust framework for understanding alpha/beta-hydrolase diversity and evolution.
• The study highlights the structural and evolutionary interconnectedness of the alpha/beta-hydrolase superfamily.
• This comprehensive analysis facilitates the exploration of sequence-structure-function relationships, aiding in the rational design of enzymes for biotechnological applications.