Serine recombinases exchange strand by “subunit exchange”
First, double strand breaks are formed by the attack of the active site serines on the scissile phosphate groups, creating covalent protein-DNA linkages and 2nt 3′ overhangs. Then half of the tetramer rotates relative to the other half, facilitated by the flat, hydrophobic central interface.
The Ccr recombinases encoded by the SCCmec element, as well as Sin (see below) belong to this family.
movie credits: Phoebe Rice and Ross Keenholtz
Cch, a conserved protein encoded by SCCmec elements
By sequence analysis, we found that SCC elements always encode a putative helicase upstream from their recombinases, and that it is related to the self-loading initiator helicases of the SaPIs – a different family of genomic island that infests S. aureus.
By structural analysis, we found that this helicase, Cch, is related to the archaeal/eukaryotic helicase MCM rather than the bacterial DnaB.
Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative. Mir-Sanchis I, Roman CA, Misiura A, Pigli YZ, Boyle-Vavra S, Rice PA. Nat Struct Mol Biol. 2016 Oct;23(10):891-898. doi: 10.1038/nsmb.3286.
Crystal structure of the Mu transpososome
The μ transpososome structure sheds light on DDE recombinase evolution. Montaño SP, Pigli YZ, Rice PA. Nature. 2012 Nov 15;491(7424):413-7. doi: 10.1038/nature11602.
Model of the Sin synaptosome
Sin is a site-specific recombinase from the Serine family. It is found on ~50% of all staphylococcal plasmids, and provides stability to those plasmids by resolving dimers back into monomers. (Such dimers form during RecA-mediated repair of stalled replication forks).
Sin is regulated by DNA topology: the tetramer on the left side in this movie is only active when in the context of this larger complex. Dependence on this “synaptosome” harnesses supercoiling as a driving force for subunit rotation, ensures that the crossover sites will be aligned in the correct orientation, and ensures that recombination can only intramolecularly (within one dimeric plasmid rather than between two monomeric ones).
Architecture of a serine recombinase-DNA regulatory complex. Mouw KW, Rowland SJ, Gajjar MM, Boocock MR, Stark WM, Rice PA. Mol Cell. 2008 Apr 25;30(2):145-55. doi: 10.1016/j.molcel.2008.02.023.