2ITJ

Origin binding domain of the SV40 large T antigen (residues 131-259). P212121 crystal form

Summary for 2ITJ

• Entry DOI: 10.2210/pdb2itj/pdb
• Related: 2IPR 2ITL 2NL8
• Descriptor: large T antigen (2 entities in total)
• Functional Keywords: dna binding protein
• Biological source: Simian virus 40
• Cellular location: Host nucleus: P03070
• Total number of polymer chains: 2
• Total formula weight: 30761.41

Authors

Martynowski, D.,Bochkareva, E.,Bochkarev, A. (deposition date: 2006-10-19, release date: 2006-12-12, Last modification date: 2023-08-30)

Primary citation

Bochkareva, E.,Martynowski, D.,Seitova, A.,Bochkarev, A.
Structure of the origin-binding domain of simian virus 40 large T antigen bound to DNA
Embo J., 25:5961-5969, 2006

PubMed 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.

PubMed: 17139255
DOI: 10.1038/sj.emboj.7601452

Experimental method

X-RAY DIFFRACTION (2.5 Å)