Arm-site binding by lambda -integrase: solution structure and functional characterization of its amino-terminal...

Area of Science:

• Molecular Biology
• Structural Biology
• Virology

Background:

• Bacteriophage lambda integrase (Int) mediates viral DNA integration/excision in E. coli.
• Int belongs to the lambda-Int family of site-specific recombinases with dual DNA-binding domains.
• The protein's function involves distinct carboxyl-terminal (catalytic) and amino-terminal (DNA-binding) domains.

Purpose of the Study:

• To determine the minimal DNA-binding domain of Int responsible for recognizing phage arm sites.
• To elucidate the solution structure of this minimal DNA-binding domain.
• To understand the structural basis of DNA-site recognition by the integrase protein.

Main Methods:

• Nuclear Magnetic Resonance (NMR) spectroscopy was used to determine the solution structure.
• Characterization of the minimal DNA-binding domain, INT-DBD(1-64) (residues Met-1 to Leu-64).
• Comparative analysis with other DNA-binding proteins and domains.

Main Results:

• Residues Met-1 to Leu-64 define the minimal arm-type DNA-binding domain (INT-DBD(1-64)).
• The INT-DBD(1-64) structure is a novel three-stranded beta-sheet DNA-binding protein.
• A disordered amino-terminal basic tail is essential for arm-site binding, supplementing the beta-sheet motif.

Conclusions:

• The structure of INT-DBD(1-64) reveals a new class of DNA-binding proteins.
• The disordered tail plays a critical role in the specific recognition of phage DNA sites.
• This structural insight aids in understanding the mechanism of lambda integrase-mediated recombination.