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Multicopper oxidases: modular structure, sequence space, and evolutionary relationships.

Maike Gräff1, Patrick C F Buchholz1, Marilize Le Roes-Hill2

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|May 25, 2020
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Summary

Multicopper oxidases (MCOs) are crucial enzymes for lignin degradation and industrial applications. This study systematically analyzed MCO sequences and structures, revealing conserved domains and binding sites for improved enzyme engineering.

Keywords:
Laccase and multicopper oxidase engineering databaseLccEDdata miningsequence alignmentsequence-structure-function relationshipstandard numbering

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Area of Science:

  • Biochemistry
  • Enzymology
  • Structural Biology

Background:

  • Multicopper oxidases (MCOs) are copper-containing enzymes that catalyze substrate oxidation and oxygen reduction to water.
  • Fungal MCOs are particularly relevant for lignin degradation, with potential applications in biofuels and industry.
  • MCOs exhibit structural diversity, classified into two-, three-, and six-domain types based on their protein architecture.

Purpose of the Study:

  • To systematically compare sequences and structures of MCOs from the updated Laccase and Multicopper Oxidase Engineering Database.
  • To identify conserved domains, numbering schemes, and copper-binding motifs within MCOs.
  • To elucidate evolutionary relationships and enable family-specific annotation of MCOs.

Main Methods:

  • Systematic comparison of 51,058 MCO sequences and 229 structures.
  • Development of standard numbering schemes for copper-binding domains (N and C).
  • Analysis of protein sequence networks to infer evolutionary relationships.

Main Results:

  • All MCOs comprise cupredoxin-like domains (N, C, and M).
  • Established standard numbering schemes for domains N and C, identifying conserved positions.
  • Identified two sequence motifs for copper binding sites per domain and demonstrated modularity of the T1-copper binding site.
  • Protein sequence networks revealed relationships between two- and three-domain MCOs.

Conclusions:

  • The study provides a comprehensive structural and sequence-based classification of MCOs.
  • Identified conserved motifs and numbering schemes facilitate MCO engineering and functional studies.
  • Understanding MCO modularity and evolutionary relationships aids in discovering and annotating new MCO families for biotechnological applications.