Structural basis of sequence-specific Holliday junction cleavage by MOC1

Area of Science:

• Molecular Biology
• Structural Biology
• Genetics

Background:

• Holliday junctions (HJs) are crucial intermediates in homologous recombination and DNA repair.
• Efficient resolution of HJs by resolvases is vital for maintaining genome stability.
• Mechanisms of sequence-specific substrate recognition and cleavage by resolvases are not fully understood.

Purpose of the Study:

• To elucidate the structural basis of sequence-specific Holliday junction recognition and cleavage by the monokaryotic chloroplast 1 protein (MOC1).
• To understand how MOC1 achieves catalytic efficiency through substrate specificity.

Main Methods:

• X-ray crystallography of MOC1 alone and bound to HJ DNA.
• Biochemical analyses.
• Molecular dynamics simulations.

Main Results:

• Determined crystal structures of MOC1 from Zea mays, revealing a unique β-hairpin for DNA junction binding.
• Identified a base-recognition motif that interacts with the junction center, inducing base flipping and pseudobase-pair formation.
• Structures and simulations support a two-metal ion catalysis mechanism, linking substrate recognition to catalytic activity.

Conclusions:

• MOC1 employs a distinct structural mechanism for sequence-specific HJ recognition and cleavage.
• A communication pathway exists between substrate recognition and metal ion-dependent catalysis in MOC1.
• This study provides insights into how resolvases achieve catalytic efficiency through specific DNA binding.