SNAP output for PDB entry 4zq9 [SNAP web server]

PDB-id

4zq9; SNAP-derived features in text and JSON formats; DNAproDB

Class

DNA binding protein-DNA

Method

X-ray (2.6 Å)

Summary

X-ray structure of aav-2 obd bound to aavs1 site 3:1

Reference

Musayev FN, Zarate-Perez F, Bishop C, Burgner JW, Escalante CR (2015): "Structural Insights into the Assembly of the Adeno-associated Virus Type 2 Rep68 Protein on the Integration Site AAVS1." J.Biol.Chem., 290, 27487-27499. doi: 10.1074/jbc.M115.669960.

Abstract

Adeno-Associated virus (AAV) is the only eukaryotic virus with the property of establishing latency by integrating site-specifically into the human genome. The integration site known as AAVS1 is located in chromosome 19 and contains multiple GCTC repeats that are recognized by the AAV non-structural Rep proteins. These proteins are multifunctional, with an N-terminal origin-binding domain (OBD) and a helicase domain joined together by a short linker. As a first step to understand the process of site-specific integration, we set up to characterize the recognition and assembly of Rep68 onto the AAVS1 site. We first determined the X-ray structure of AAV-2 Rep68 OBD in complex with the AAVS1 DNA site. Specificity is achieved through the interaction of a glycine-rich loop that binds the major groove and an α-helix that interacts with a downstream minor groove on the same face of the DNA. Although the structure shows a complex with three OBD molecules bound to the AAVS1 site, we show using analytical centrifugation and electron microscopy that the full length Rep68 forms a heptameric complex. Moreover, we determine that a minimum of two direct repeats is required to form a stable complex and melt DNA. Finally, we show that although the individual domains bind DNA poorly, complex assembly requires oligomerization and cooperative between its OBD, helicase and the linker domains.