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Studies of bacteriophage Mu transposition paved the way for understanding retroviral integration and V(D)J recombination as well as many other DNA transposition reactions. Here we report the structure of the Mu transpososome--Mu transposase (MuA) in complex with bacteriophage DNA ends and target DNA--determined from data that extend anisotropically to 5.2 Å, 5.2 Å and 3.7 Å resolution, in conjunction with previously determined structures of individual domains. The highly intertwined structure illustrates why chemical activity depends on formation of the synaptic complex, and reveals that individual domains have different roles when bound to different sites. The structure also provides explanations for the increased stability of the final product complex and for its preferential recognition by the ATP-dependent unfoldase ClpX. Although MuA and many other recombinases share a structurally conserved 'DDE' catalytic domain, comparisons among the limited set of available complex structures indicate that some conserved features, such as catalysis in trans and target DNA bending, arose through convergent evolution because they are important for function. The structure of the bacteriophage transposase MuA bound to DNA sequences that mimic both the transposon ends and the target DNA ends is solved; the picture of this synaptic complex illustrates the intricacy of Mu transposition, and exposes the architectural diversity among DDE recombinases in complex with substrate DNAs. Phage transpososome structure determined DNA sequences known as transposons encode proteins that allow them to insert copies of themselves throughout the genome. The mechanism of transposition has similarities to processes involved in retroviral integration and during immunoglobulin and T-cell-receptor development. Phoebe Rice and colleagues have now solved the structure of a bacteriophage transposase (MuA) bound to DNA sequences that mimic both the transposon ends and the target DNA ends. Images of this synaptic complex show the roles that individual domains of MuA have, and highlight the benefits provided by the intertwined structure., Author(s): Sherwin P. Montaño [sup.1] , Ying Z. Pigli [sup.1] , Phoebe A. Rice [sup.1] Author Affiliations: (1) Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, USA [...]

The eubacterial SOS system is a paradigm of cellular DNA damage and repair, and its activation can contribute to antibiotic resistance (1-3). Under normal conditions, LexA represses the transcription of many DNA repair proteins by binding to SOS 'boxes' in their operators. Under genotoxic stress, accumulating complexes of RecA, ATP and single-stranded DNA (ssDNA) activate LexA for autocleavage. To address how LexA recognizes its binding sites, we determined three crystal structures of Escherichia coli LexA in complex with SOS boxes. Here we report the structure of these LexA-DNA complexes. The DNA-binding domains of the LexA dimer interact with the DNA in the classical fashion of a winged helix-turn-helix motif. However, the wings of these two DNA-binding domains bind to the same minor groove of the DNA. These wing-wing contacts may explain why the spacing between the two half-sites of E. coli SOS boxes is invariant., The LexA protein contains two domains: an amino-terminal winged helix-turn-helix (wHTH) DNA-binding domain, and a carboxy-terminal dimerization and latent protease domain (Fig. 1 and Supplementary Fig. 1). The structure of [...]