The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases

Area of Science:

• Biochemistry
• Bioinformatics
• Protein Science

Background:

• Multicopper oxidases (MCOs), including laccases, are enzymes catalyzing oxidation reactions with significant biotechnological potential.
• Understanding the diversity and relationships within the MCO superfamily is crucial for their effective application.

Purpose of the Study:

• To develop a systematic, sequence-based classification and analysis tool for the multicopper oxidase protein family.
• To create a comprehensive resource integrating sequence and structural information for MCOs.

Main Methods:

• Development of the Laccase Engineering Database (LccED) for protein classification.
• Utilizing sequence alignments, phylogenetic trees, HMM profiles, and structural data for analysis.
• Classification of over 2200 MCO proteins into superfamilies and homologous families.

Main Results:

• The LccED successfully classified more than 2200 MCO proteins into 11 superfamilies and 56 homologous families.
• The database provides tools for comparative analysis of sequences and structures, revealing biochemical properties.
• Investigation into the distribution of MCOs across different kingdoms was performed.

Conclusions:

• The LccED serves as a valuable classification tool for assigning new MCOs to homologous families.
• The database facilitates the exploration of sequence-structure-function relationships.
• LccED aids in guiding protein engineering efforts for MCOs and laccases.