Two tricks in one bundle: helix-turn-helix gains enzymatic activity

Area of Science:

• Molecular Biology
• Biochemistry
• Structural Biology

Background:

• Enzymes typically lose catalytic activity to gain other functions; the reverse is rare.
• Structural similarity between lambda integrase (Int) family and AraC transcriptional activators suggests a shared evolutionary origin.
• The Int family likely evolved from duplicated DNA-binding homeodomain-like modules that acquired enzymatic functions.

Purpose of the Study:

• To investigate the evolutionary origins of the Int protein family.
• To understand the structural basis of catalytic activity in Int proteins and related enzymes.
• To explore the parallel evolution of enzymatic function in homologous DNA-binding domains.

Main Methods:

• Comparative structural analysis of Int proteins and related DNA-modifying enzymes.
• Identification of conserved structural motifs, including helix-turn-helix (HTH) domains.
• Mapping of catalytic residues within the active sites of various tyrosine DNA-breaking/rejoining enzymes.

Main Results:

• Int proteins possess two HTH motifs involved in both DNA binding and catalysis.
• The active site of Int proteins, including type IB topoisomerases, is located at the domain interface.
• Catalytic tyrosine residues in homologous HTH domains of various 'tyrosine' recombinases are found in non-conserved structural positions, indicating parallel evolution.

Conclusions:

• The Int family represents a rare example of enzymes evolving from DNA-binding modules.
• Homologous HTH domains evolved similar catalytic mechanisms independently, with catalytic residues located at non-homologous sites.
• This study highlights a unique case of parallel evolution in enzymatic domain function and structure.