Viral integration of bacteriophage has been the subject of intense study for many years, particularly in the phages Lambda and P1 [1]. Integration is a feature strongly selected for by many viruses, as shown by the conservation the tyrosine recombinase family of integrases in viruses infecting all domains of life [2]. Integration is not only a driving force in lateral gene transfer within and between species [3-6], it also allows the phage to integrate into its host and may enhance the odds of the survival of its genetic information.
Site-specific integration in many viruses is accomplished by integrases in the tyrosine recombinase family of proteins. This family of integrases is distinctly different from the relatively non-specific retroviral integrases, transposases, and recombinases used by viruses such as Phage Mu and HIV as well as various insertion elements. While these protein complexes carry out essentially the same chemistry to recombine DNA, the mechanisms used are unique, and the protein families involved do not show homology to each other (for a description of the differences see [7] Chapter 2, pp 13-22).
Members of the tyrosine recombinase protein family span a large range of functions, such as topoisomerases, resolvases, restriction endonucleases, and regulators of gene expression [2]. The hallmark trait of tyrosine recombinases is a tetrad of non-consecutive amino acid residues (Arg-His-Arg-Tyr) present in the catalytic site. Studies of the crystal structures of Lambda and Cre recombinase shows that the basic Arg-His-Arg residues are involved in coordinating the DNA so that the scissile phosphate of the DNA backbone is aligned with the active tyrosine, the fourth conserved residue [8]. A transesterification by the scissile phosphate is accomplished by a nucleophilic attack of the tyrosine residue, which acts an intermediate while transferring the bond in a manner analogous to that used by topoisomerase IB. Monomers of integrase therefore have one active site per peptide, so four monomers are needed to completely recombine two strands of DNA [9]. Recombination of the strands occurs by the formation and resolution of a Holliday junction, as seen in the crystal structures of Cre Recombinase and Lambda integrase [10, 11].
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