Flexibility of KorA, a plasmid-encoded, global transcription regulator, in the presence and the absence of its operator

The IncP (Incompatibility group P) plasmids are important carriers in the spread of antibiotic resistance across Gram-negative bacteria. Gene expression in the IncP-1 plasmids is stringently controlled by a network of four global repressors, KorA, KorB, TrbA and KorC interacting co-operatively. Intriguingly, KorA and KorB can act as co-repressors at varying distances between their operators, even when they are moved to be on opposite sides of the DNA. KorA is a homodimer with the 101-aminoacid subunits, folding into an N-terminal DNA-binding domain and a C-terminal dimerisation domain. In this study, we have determined the structures of the free KorA repressor and two complexes each bound to a 20 bp palindromic DNA duplex containing its consensus operator sequence. Using a combination of X-ray crystallography, NMR spectroscopy, SAXS and molecular dynamics calculations, we show that the linker between the two domains is very flexible and the protein remains highly mobile in the presence of DNA. This flexibility allows the DNA-binding domains of the dimer to straddle the operator DNA on binding and is likely to be important in co-operative binding to KorB. Unexpectedly, the C-terminal domain of KorA is structurally similar to the dimerisation domain of the tumour suppressor p53.