Structural Basis of the Role of the NikA Ribbon-Helix-Helix Domain in Initiating Bacterial Conjugation

Conjugation is a fundamental process for the rapid evolution of bacteria, enabling them, for example, to adapt to various environmental conditions or to acquire multi-drug resistance. NikA is one of the relaxosomal proteins that initiate the intercellular transfer of the R64 conjugative plasmid with the P-type origin of transfer, oriT. The three-dimensional structure of the N-terminal 51 residue fragment of NikA, NikA(1–51), which binds to the 17-bp repeat A sequence in R64 oriT, was determined by NMR to be a homodimer composed of two identical ribbon-helix-helix (RHH) domains, which are commonly found in transcriptional repressors. The structure determination of NikA(1–51) was achieved using automated NOE assignment with CYANA, without measuring filtered NOESY experiments to distinguish between the intra- and intermolecular NOEs, and without any a priori assumption on the tertiary or quaternary structure of the protein. Mutational experiments revealed that the DNA-binding region of the NikA(1–51) dimer is an anti-parallel β-sheet composed of one β-strand from each of the N-terminal ends of the two domains. Various biochemical experiments have indicated that the full length NikA(1–109) exists as a homotetramer formed through an α-helical domain at the C-terminus, and that the anti-parallel β-sheets of both dimeric domains bind to two homologous 5 bp internal repeats within repeat A. As a tetramer, the full length NikA(1–109) showed higher affinity to repeat A and bent the oriT duplex more strongly than NikA(1–51) did. Many RHH proteins are involved in specific DNA recognition and in protein–protein interactions. The discovery of the RHH fold in NikA suggests that NikA binds to oriT and interacts with the relaxase, NikB, which is unable to bind to the nick region in oriT without NikA.