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In site-specific recombination, DNA molecules are cleaved in both strands at two separate recombinase binding sites, and the ends are rejoined to new partners, without any synthesis or degradation of DNA or hydrolysis of phosphodiesters. Site-specific recombinases mediate a wide range of microbial programmed DNA rearrangements.

There are two families of site-specific recombinases :
1. The resolvase/invertase family use a serine nucleophile to mediate a concerted double strand cleavage and rejoining reaction ay nucleotide phosphates separated by 2 bp
2. The lambda integrase family enzymes use a tyrosine nucleophile to mediate sequential pairs of strand exchanges that are positioned 6-8 bp apart.

Xer site specific recombination exhibits three features that distinguish it from other well characterised members of the family.
1. It uses two related recombinases, XerC and XerD, each of which catalyses one specific pair of strand exchanges.
2. The recombination reaction has different requirements and outcomes depending on whether it occurs at plasmid or chromosomal recombination sites.
3. Despite the sequence divergence of integrase family recombinases, conserved Xer-like recombinase sequences are present in the chromosomes of almost all bacteria suggesting that there is a strong constraint on how Xer recombination functions in chromosome segregation.

The site-specific recombinase XerD belongs to the lambda integrase family of enzymes. The crystal structure (below) of XerD has been solved at 2.5 Å resolution. The structure shows two distinct domains. The domain 1 consists of residues 1-107, while domain 2 comprises residues 108-298.