Four Parallel Pathways in T4 Ligase-Catalyzed Repair of Nicked DNA with Diverse Bending Angles

The structural diversity of biological macromolecules in different environments contributes complexity to enzymological processes vital for cellular functions. Fluorescence resonance energy transfer and electron microscopy are used to investigate the enzymatic reaction of T4 DNA ligase catalyzing the ligation of nicked DNA. The data show that both the ligase-AMP complex and the ligase-AMP-DNA complex can have four conformations. This finding suggests the parallel occurrence of four ligation reaction pathways, each characterized by specific conformations of the ligase-AMP complex that persist in the ligase-AMP-DNA complex. Notably, these complexes have DNA bending angles of approximate to 0 degrees, 20 degrees, 60 degrees, or 100 degrees. The mechanism of parallel reactions challenges the conventional notion of simple sequential reaction steps occurring among multiple conformations. The results provide insights into the dynamic conformational changes and the versatile attributes of T4 DNA ligase and suggest that the parallel multiple reaction pathways may correspond to diverse T4 DNA ligase functions. This mechanism may potentially have evolved as an adaptive strategy across evolutionary history to navigate complex environments. Fluorescence resonance energy transfer and electron microscopy are used to unlock the intricacies of T4 DNA ligase catalysis of nicked DNA ligation. Four distinct conformations of both the ligase-AMP and ligase-AMP-DNA complexes are discovered, suggesting parallel ligation pathways. These findings underscore the conformational versatility of T4 DNA ligase, suggesting multiple reaction pathways as adaptive strategies for DNA with diverse bending angles. image