SNAP output for PDB entry 2nl8 [SNAP web server]

PDB-id

2nl8; SNAP-derived features in text and JSON formats; DNAproDB

Class

DNA binding protein-DNA

Method

X-ray (2.3 Å)

Summary

The origin binding domain of the sv40 large t antigen bound non specifically to a 17 bp palindrome DNA (sites 1 and 3)

Reference

Bochkareva E, Martynowski D, Seitova A, Bochkarev A (2006): "Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA." Embo J., 25, 5961-5969. doi: 10.1038/sj.emboj.7601452.

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.