Modeling of the full-length Escherichia coli SeqA protein, in complex with DNA

The Escherichia coli SeqA protein, a negative regulator of chromosome DNA replication, prevents the overinitiation of replication within one cell cycle by binding to hemimethylated GATC sequences in the replication origin, oriC. In addition to the hemimethylated DNA-binding activity, the SeqA protein has a self-association activity, which is also considered to be essential for its regulatory function in replication initiation. To study the SeqA protein biological activity, we performed a SeqA protein model to examine its architecture. SeqA has a bipartite structure composed of a large and small lobe. The SeqA spatial conformation contributes to its ability to bind to a pair of hemimethylated GATC sequences and to its cooperative behavior.