(A) Formation of the integrated prophage. In those infected cells where the decision has been made not to replicate the viral DNA, the circularized supercoiled viral DNA (black lines) is inserted into the bacterial chromosome (curly red lines) at a specific site (called attB or BOB’) located between the gal and bio genes (Campbell, 1963). This insertion, integrative recombination, involves cutting the viral DNA at a specific site (called attP or P’C’OCP) and joining these cut ends to the cut ends of the bacterial chromosome in attB. The cutting, recombining, and resealing of viral and bacterial DNA generates new DNA sequences forming the junctions between bacterial and integrated viral DNA. These junction sequences, called attL (BOC’P’) and attR (PCOB’) on the left and right respectively, are themselves substrates for the cutting, recombining, and resealing reactions that will, sometime in the future, remove (excise) the viral DNA from the host chromosome and thereby regenerate the viral attP and bacterial attB sequences. The integrated provirus chromosome is stably inherited, with almost all of its genes repressed, for many bacterial generations. Upon instigation by the appropriate physiological signals, the viral chromosome is excised, replicated, and inserted into viral particles which are released into the environment. The integrative reaction requires the virally-encoded integrase protein (Int) and the bacterial accessory protein Integration Host Factor (IHF). The excisive reaction additionally requires the virally encoded accessory protein Xis (which also inhibits the integrative reactions). Both reactions are stimulated by the bacterial accessory protein Fis. (See Panel C for DNA binding sites of all the proteins and their respective roles in each reaction). Both reactions proceed through a four-way DNA junction called a Holliday junction (HJ) (see Panel B for details of these DNA strand exchanges) (reviewed in [Landy, 2015]). (B) The Holliday junction intermediate. Cutting, recombining, and resealing DNA during recombination proceeds by two pairs of sequential single-strand DNA exchanges that are staggered by seven base pairs that are identical in all four att sites; they are referred to as the 'overlap' region (O). The molecular details of this recombination are common to all reactions catalyzed by the large family of tyrosine recombinases (except for the size of the O regions and the order of strand exchanges), as first characterized for λ Int, Cre, Flp, and XerC/D (reviewed in [Van Duyne, 2015]). It proceeds in the absence of exogenous energy via the formation of high-energy covalent 3’phospho-tyrosine intermediates in the active site of each Int protein. Illustrated here is the pathway for integrative recombination; it would be identical for the excisive reaction but the substrates (left panel) would be attL and attR, leading to attP and attB products (right panel). Viral and bacterial DNAs are denoted as in panel A. (i) The attP (C’OC) and attB (BOB’) sites are aligned anti-parallel with respect to their identical overlap sequences. (ii) The first pair of exchanges, always at the C (green) and B (blue) core sites, is initiated by formation of 3’ phospho-tyrosine linkages (with Tyr342) and 5’ OH termini. (iii) The 5’ OH terminus generated by the cleavage at C attacks the phospho-tyrosine linkage at B to regenerate a new B–C’ strand (orange arrow head). Concomitantly, the 5’ OH from the cleavage at C attacks the phospho-tyrosine linkage at B to regenerate a new B'–C strand (orange arrow head). Together, this pair of single strand exchanges, at one boundary of the overlap region, forms the four-way DNA (HJ) intermediate. (iv) A similar pair of single strand cleavage, exchange, and resealing reactions is executed by the Ints at C’ (brown) and B’ (purple) on the other side of the overlap region. (v) As a result of the two sequential pairs of single-strand exchanges, all four DNA strands have new junction sequences and the HJ is resolved to recombinant products attL (C’OB) and attR (COB’). C) Additional complexity, in the P’ and P arms, confers regulation and directionality to the λ Int reaction. In contrast to the 'simple' Cre and Flp tyrosine recombinases, λ Int (and more than a thousand viral cousins in the public data bases) has two DNA binding domains, as shown in Figure 2. The carboxy-terminal domain of Int (CTD) binds at the four sites of DNA cleavage (called core-type sites; blue boxes) and catalyzes the chemistry of DNA cleavage and rejoining; this domain and the core-type sites (B, B’, C’ and C) are analogous, and very similar, to the Cre and Flp enzymes and their respective DNA targets sites (see panel B). In λ Int an additional small DNA binding domain at the amino terminus (NTD) binds with high affinity to a different family of DNA sequences (arm-type sites) (green boxes) distant from the sites of DNA cleavage and located in the P’ and P arms of viral DNA (adjacent to C’ and C, respectively). To enable the ('hetero-bivalent') Int to bind simultaneously to both of its DNA targets the core- and arm-type DNA sites are interposed by binding sites for the accessory DNA bending proteins, IHF (yellow boxes, H1, H2, and H’), Xis (gold boxes, X1, X1.5, X2), and Fis (magenta). The DNA bending proteins bring the core- and arm-type sites into close proximity and also serve as essential elements in forming the large multi-protein recombination complexes. Two distinct but overlapping ensembles of binding sites are employed (solid boxes) to generate either the integrative or excisive recombinogenic complexes (reviewed in [Landy, 2015]). (For the patterns of Int bridging between core- and arm-type sites in each of the complexes see Figure 2).