Structure-function correlations in the XerD site-specific recombinase revealed by pentapeptide scanning mutagenesis

Xer-mediated site-specific recombination contributes to the stability of circular chromosomes in bacteria by resolving plasmid multimers and chromosome dimers to monomers prior to cell division. Two related site-specific recombinases, XerC and XerD, each catalyse one pair of strand exchange during Xer recombination. In order to relate the recently determined structure of XerD to its function, the XerD protein was subjected to pentapeptide scanning mutagenesis, which leads to a variable five amino acid cassette being introduced randomly into the target protein. This has allowed identification of regions of XerD involved in specific DNA binding, in communicating with the partner recombinase, XerC, and in catalysis and its control. The C-terminal domain of XerD, comprising two-thirds of the protein, contains the catalytic active site and comprises ten α helices (αE to αN) and a β hairpin. A flexible linker connects this domain to the N-terminal domain that comprises four α helices (αA to αD). Pentapeptide insertions into αB, αD, αG, or αJ interfered with DNA binding. Helices αG and αJ comprise a pseudo helix-turn-helix DNA binding motif that may provide specificity of recombinase binding. An insertion in αL, adjacent to an active site arginine residue, led to loss of cooperative interactions between XerC and XerD and abolished recombination activity. Other insertions close to active site residues also abolished recombination activity. Proteins with an insertion in the β hairpin turn bound DNA, interacted cooperatively with XerC and had a phenotype that is consistent with the protein being defective in XerD catalysis. This β hairpin appears to be highly conserved in related proteins. Insertions at a number of dispersed locations did not impair XerD catalysis activity or DNA binding, but failed to allow XerC catalysis in vivo, indicating that several sites of interaction between XerD and XerC may be important for activation of XerC catalysis by XerD.