α/β Hydrolases: Toward Unraveling Entangled Classification

Area of Science:

• Biochemistry
• Structural Biology
• Bioinformatics

Background:

• Alpha/beta hydrolase-like enzymes are a large, functionally diverse protein superfamily.
• High sequence similarity among distinct families complicates accurate functional annotation and classification.
• Existing definitions overlap, hindering reliable assignment in high-throughput studies.

Purpose of the Study:

• To re-annotate protein families within the alpha/beta hydrolase-like superfamily.
• To revise the classification of this superfamily based on sequence and structural analyses.
• To develop a robust system for automatic functional annotation of superfamily members.

Main Methods:

• Manual curation of structural superimpositions.
• Multiple sequence and structure alignments.
• Pairwise sequence similarity assessments and clustering.
• Development of family profiles for annotation.

Main Results:

• Three protein families were newly annotated as alpha/beta hydrolase-like.
• Structural conservation and diversity across the superfamily were comprehensively demonstrated.
• A novel clustering of alpha/beta hydrolases was established.
• A set of family profiles for reliable functional annotation was created.

Conclusions:

• The revised classification and new annotation profiles improve the understanding of the alpha/beta hydrolase-like superfamily.
• The developed profiles enable detailed and reliable automatic functional assignments.
• This work addresses challenges in annotating functionally diverse enzymes with conserved structures.