Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA

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Abstract
The large T antigen (T‐ag) protein binds to and activates DNA replication from the origin of DNA replication ( ori ) in simian virus 40 (SV40). Here, we determined the crystal structures of the T‐ag origin‐binding domain (OBD) in apo form, and bound to either a 17 bp palindrome (sites 1 and 3) or a 23 bp ori DNA palindrome comprising all four GAGGC binding sites for OBD. The T‐ag OBDs were shown to interact with the DNA through a loop comprising Ser147–Thr155 (A1 loop), a combination of a DNA‐binding helix and loop (His203–Asn210), and Asn227. The A1 loop traveled back‐and‐forth along the major groove and accounted for most of the sequence‐determining contacts with the DNA. Unexpectedly, in both T‐ag‐DNA structures, the T‐ag OBDs bound DNA independently and did not make direct protein–protein contacts. The T‐ag OBD was also captured bound to a non‐consensus site ATGGC even in the presence of its canonical site GAGGC. Our observations taken together with the known biochemical and structural features of the T‐ag–origin interaction suggest a model for origin unwinding.