A XerD recombinase with unusual active site motifs in Streptococcus pneumoniae.

XerD belongs to the site specific recombinases of the integrase family of proteins that catalyze recombination events via a phosphotyrosine intermediate. Sequence alignments and crystal structure resolution of E. coli XerD and related enzymes demonstrated the importance of four conserved amino acids R-H-R-H that are spaced along the C-terminal domain in addition to a conserved K and the active site Y, all of which have been implicated in catalysis. The deduced amino acid sequence of the putative S. pneumoniae XerD contained three unique replacements at the conserved positions resulting in L-Q-R-L; moreover, the active site Y was the penultimate amino acid residue, and the extreme C-terminal region suggested to be involved in interaction of E. coli XerD with XerC was lacking. Severe growth defects in a loss-of-function xerD mutant are consistent with an important in vivo function of the S. pneumoniae XerD protein. Highly related xerD genes with similar unusual amino acid replacements were found in S. mitis, S. mutans and S. pyogenes but not in other Gram-positive bacteria, although the genetic environment was very similar in many species. There are at least another four genes in the S. pneumoniae KNR_7/87 genome encoding Xer related peptides, one of which was identified as the xerC homologue. The xerD and xerC genes were present in a sample of 20 S. pneumoniae strains whereas the other xer genes appear to be absent in some of the strains and are more closely related to integrases of phage and transposon origin.