Highlights • Bacterial proteins comprising solely a VRR-Nuc domain are dimeric in solution • Bacterial VRR-Nuc domains act as Holliday-junction-resolving enzymes • A conserved helical insertion in the FAN1 VRR-Nuc domain prevents dimerization • FAN1 monomers cannot cleave Holliday junctions and instead cleave 5′ flap DNA T