FC0059
Plasmid partition protein ParB  -  DNA

Biological function
The partition complex necessary for segregation, P1 ParB must recognize a complicated arrangement of A-box and B-box DNA motifs located on opposite ends of a sharply bent parS partition site of 74 bp.

Domain organization/sequence features
When ParB bound to partition sites, it forms an asymmetric dimer with extended amino-terminal HTH (helix–turn–helix) domains that contact A-boxes. The two HTH domains emanate from a dimerized DNA-binding module composed of a six-stranded β- sheet coiled-coil that binds B-boxes.

Structural evidence
The individual DNA-binding modules rotate freely about a flexible linker, ParB (142–333) consists of two independent domains that are flexibly linked and, in the two crystal forms, the domains show marked ranges of rotations that enable them to contact DNA duplexes in distinct orientations. The two domains of ParB(142–333), which are identical in the two crystal forms, are connected by a flexible linker comprising residues 271–274 and consist of an N-terminal domain, an all-helical region (the HTH domain, residues 147–270) and a dimerization domain (the ’dimer domain’, residues 275–333). No stabilizing interactions are found between the two domains. The ParB–DNA structures reveal two atypical DNA-binding features of ParB, its bridging capability and its flexibly attached DNA-binding modules.

Structure/Mechanism
Because these DNA-binding modules are flexibly attached, they can rotate freely to contact various arrangements of the A and B-boxes, so they serve as independent DNA-binding modules.

Mechanism category
Tethering

Significance
Fuzziness enables multivalent DNA binding of the A and B boxes, which could be important for organization of the initial partitioning complex and its assembly with further ParB dimers. ParB dimer binds across parS to form the initial P1 partition complex and fuzziness of ParB linker enables to bind between the looped parS arms.