Modeling of the bacterial luciferase-flavin mononucleotide complex combining flexible docking with structure-activity...

Area of Science:

• Biochemistry
• Structural Biology
• Enzymology

Background:

• The crystal structure of Vibrio harveyi luciferase is known, but substrate binding sites remain elusive.
• Understanding these sites is crucial for elucidating the mechanism of bacterial bioluminescence.

Purpose of the Study:

• To develop a structural model of the Vibrio harveyi luciferase-flavin mononucleotide complex.
• To identify the binding sites for flavin mononucleotide and fatty aldehyde substrates.

Main Methods:

• Point mutagenesis to support phosphate-binding site location.
• Flexible docking using Monte Carlo minimization.
• Filtering docked conformations using structure-activity data.
• Developing a model based on energetic and geometric constraints.

Main Results:

• A model of the luciferase-flavin mononucleotide complex was generated, consistent with experimental data.
• The flavin mononucleotide isoalloxazine ring interacts with specific residues (Ala-Ala cis-peptide, Cys 106) on the alpha subunit.
• A distinct cavity for aldehyde binding was identified adjacent to the isoalloxazine ring, involving residues His 44 and Trp 250.

Conclusions:

• The developed model provides insights into the binding of flavin mononucleotide and the location of the fatty aldehyde binding site.
• This work advances the understanding of the Vibrio harveyi luciferase active site and mechanism.
• The findings lay the groundwork for future studies on enzyme function and inhibitor design.