SNAP output for PDB entry 4fgn [SNAP web server]

PDB-id

4fgn; SNAP-derived features in text and JSON formats; DNAproDB

Class

DNA binding protein-DNA

Method

X-ray (3.2 Å)

Summary

Crystal structure of the sv40 large t-antigen origin bining domain bound to site i DNA

Reference

Meinke G, Phelan PJ, Harrison CJ, Bullock PA (2013): "Analysis of the Costructure of the Simian Virus 40 T-Antigen Origin Binding Domain with Site I Reveals a Correlation between GAGGC Spacing and Spiral Assembly." J.Virol., 87, 2923-2934. doi: 10.1128/JVI.02549-12.

Abstract

Polyomavirus origins of replication contain multiple G(A/G)GGC sequences; the high affinity binding element for the viral initiator T-antigen (T-ag). The Site I regulatory region of Simian Virus 40, involved in the repression of transcription and the enhancement of DNA replication initiation, contains two GAGGC sequences arranged head-to-tail and separated by a 7 bp AT-rich sequence. We have solved a 3.2 Å co-structure of the SV40 origin-binding domain (OBD) bound to Site I. We have also established that T-ag assembly on Site I is limited to the formation of a single hexamer. These observations have enabled an analyses of the role(s) of the OBDs bound to the Site I pentanucleotides in hexamer formation. Of interest, they reveal a correlation between the OBDs bound to Site I and a pair of OBD subunits in the previously described hexameric spiral structure. Based on these findings, we propose that spiral assembly is promoted by pentanucleotide pairs arranged in a head to tail manner. Finally, the possibility that "spiral-assembly " by OBD subunits may account for the heterogeneous distribution of pentanucleotides found in the origins of replication of polyomaviruses is discussed.