DNA-binding functions of PepA

Biological background

E. coli PepA acts as a assessory protein in Xer site specific DNA recombination. Plasmid multimers are formed in E. coli by homologous recombination. These plasmid multimers reduce the number of independent plasmids and increase the chance of forming plasmid-free daughter cells at cell division. The Xer system resolves plasmid multimers, but does not form new multimers, i.e. the recombination reaction is exclusively intramolecular. For this selectivity the assessory proteins PepA and the arginine repressor (ArgR) are involved in addition to the two recombinases XerC and XerD.

In addition to this function, PepA has an independent role in the transcriptional regulation of the carAB operon, which encodes the enzyme carbamoylphosphate synthetase. For both functions interaction of PepA with DNA has been demonstrated.
 

DNA-binding groove of PepA

The molecular surface of PepA reveals a groove which runs from one trimer face along the two-fold molecular axis to the other trimer face. The model shown here demonstrates that this groove is large enough to accomodate duplex DNA.  When the DNA winds around PepA in the direction of the three-fold axis (from top to bottom in this figure), the topology of the hexamer directs the DNA strand to form a right-handed superhelix. This is in agreement with the formation of right-handed catenanes as plasmid products.

A model for the Xer complex

Based mainly on the topology of the plasmid products (4-noded, right-handed catenanes), DNase I footprinting assays and the X-ray structures of PepA and ArgR, a new model for the Xer complex was proposed by us, in which two PepA molecules (blue) and one arginine repressor (green) associate along the trimer faces. The  two recombination sequences (red and yellow) are wound around the protein complex such that right-handed superhelices are formed and three nodes are trapped. An additional node is introduced in the recombination reaction. Models were build for these complexes in order to have a realistic estimation of the relative positions of the protein binding sites along the DNA sequence and to ensure that the DNA curvature has realistic values.

References
Sträter, N., Sherratt, D. J. & Colloms, S. D. (1999). X-ray structure of aminopeptidase A from E. coli and a model for the nucleoprotein complex in Xer site-specific recombination. EMBO J. 18, 4513-4522.

Colloms, S. D., Bath, J. & Sherratt, D. J. (1997). Topological selectivity in Xer site-specific recombination. Cell 88, 855-864.