FC0058
Plasmid partition protein KorB  -  DNA

Biological function
The partitioning of DNA between daughter cells upon cell division is critical for the survival of all organisms. Partitioning in most bacteria is dependent on two proteins from the ParA/ParB families. ParB binds to a specific centromere- like sequence (parS) on the chromosome forming a higher order nucleoprotein complex that is thought to pair the sister chromosomes/plasmids. ParA, an ATPase, binds to ParB and is thought to act as a motor, pulling or pushing two ParB-bound chromosomes apart to different poles of the bacterial cell. One of the best characterized ParB proteins is KorB. KorB binds simultaneously with RNA polymerase at promoters and interacts with it to prevent open complex formation. KorB can act upstream or downstream of the promoters and also at a distance. At all promoters, KorB acts cooperatively with a second repressor, either KorA, TrbA, or KorC, forming a regulatory network that coordinates expression of the operons on the plasmid. The plasmid partition protein KorB has a dual role: it is essential for the correct segregation of the low copy number broad host range RK2 plasmid while also being an important regulator of transcription. KorB belongs to the ParB family of proteins, and partitioning in RK2 has been studied as a simplified model of bacterial chromosome segregation.

Domain organization/sequence features
KorB consists of three distinct segments of which only two have been crystallized and their structures determined to atomic resolution. The C-terminal 64 amino acid residue dimerization domain (residues 294–358). The central domain (residues 137– 252) interacts with operator DNA. The N-terminal 137 amino acids of KorB is disordered.

Structural evidence
KorB was reconstructed from the known crystal structures using small angle x-ray scattering (SAXS). The calculated an ensemble of conformation which the protein adopts in solution shows that the flexible linker region adopts a slightly more compact conformations rather than the full range of random conformers available. Flexibility is important for the protein’s functional role in the cell enabling it to bind at different distances along DNA and to different binding partners.

Biochemical evidence
The N-terminal region of KorB modulates DNA-binding strength and site selectivity, repression at a distance, as well as the localization of KorB in the cell. The region between the C-terminal domain and the central domain (residues 252–294) is implicated in several functions of KorB, including repression of transcription and cooperativity with other proteins.

Structure/Mechanism
The intrinsically disordered domain provides KorB a wide set of possible conformers available as templates for binding to a diverse set of proteins such as KorA, IncC, and RNA polymerase. Such binding events will have an effect on the ensemble of conformations KorB can adopt in solution and thus mediate the set of conformers available for interaction to a second binding partner, e.g. DNA or a third protein. The flexibility allows binding to occur at different distances between KorB and a second repressor while the conformational changes give rise to the cooperative effects. The disordered regions are also likely to be important for DNA partitioning, as many of the partition proteins need to span two DNA duplexes (or several proteins) to carry out their function. Flexible interactions between the central and C-terminal domains of a ParB protein have been seen in the crystal structures of central and C-terminal domains of ParB from P1 plasmid of Escherichia coli bound to different target sequences.

Mechanism category
Tethering

Significance
Fuzziness enables binding to a diverse set of proteins resulting in cooperative effects or different target DNA sequences. Structural plasticity might also be required for partitioning to span between two sister plasmids.