SNAP output for PDB entry 3vw4 [SNAP web server]

PDB-id

3vw4; SNAP-derived features in text and JSON formats; DNAproDB

Class

DNA binding protein-DNA

Method

X-ray (2.7 Å)

Summary

Crystal structure of the DNA-binding domain of cole2-p9 rep in complex with the replication origin

Reference

Itou H, Yagura M, Shirakihara Y, Itoh T (2015): "Structural Basis for Replication Origin Unwinding by An Initiator-Primase of Plasmid ColE2-P9: Duplex DNA Unwinding by A Single Protein." J.Biol.Chem., 290, 3601-3611. doi: 10.1074/jbc.M114.595645.

Abstract

Duplex DNA is generally unwound by protein oligomers prior to replication. The Rep protein of plasmid ColE2-P9 (34 kDa) is an essential initiator for plasmid DNA replication. This protein binds the replication origin (Ori) in a sequence specific manner as a monomer and unwinds DNA. Here we present the crystal structure of the DNA-binding domain of Rep (E2Rep-DBD) in complex with Ori DNA. The structure unveils the basis for Ori specific recognition by the E2Rep-DBD and also reveals that it unwinds DNA by the concerted actions of its three contiguous structural modules. The structure also shows that the functionally unknown PriCT domain, which forms a compact module, plays a central role in DNA unwinding. The conservation of the PriCT domain in the C-termini of some archaeo-eukaryotic primases, indicates that it likely plays a similar role in these proteins. Thus, this is the first report providing the structural basis for the functional importance of the conserved PriCT domain and also reveals a novel mechanism for DNA unwinding by a single protein.