1. Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, Oregon 97239-3098, USA
2. Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
3. †Present address: M. D. Anderson Cancer Center, Department of Biochemistry & Molecular Biology, Unit 1000, 1515 Holcombe Boulevard, Houston, Texas 77030, USA

Correspondence to: Maria A. Schumacher^1,3 Correspondence and requests for materials should be addressed to M.A.S. (Email: schumacm@ohsu.edu). The X-ray crystallographic coordinates and structure factor files have been deposited with the Protein Data Bank under accession code 1ZX4.

Abstract

The faithful inheritance of genetic information, which is essential for all organisms, requires accurate DNA partition (segregation) at cell division. In prokaryotes, partition is mediated by par systems, for which the P1 plasmid system of Escherichia coli is a prototype comprising a partition site and two proteins, ParA and ParB^{1, 2}. To form the partition complex necessary for segregation, P1 ParB must recognize a complicated arrangement of A-box and B-box DNA motifs located on opposite ends of a sharply bent parS partition site of 74 bp (refs 3–7). Here we describe structures of ParB bound to partition sites. ParB forms an asymmetric dimer with extended amino-terminal HTH (helix–turn–helix) domains that contact A-boxes. The two HTH domains emanate from a dimerized DNA-binding module composed of a six-stranded -sheet coiled-coil that binds B-boxes. Strikingly, these individual DNA-binding modules rotate freely about a flexible linker, enabling them to contact several arrangements of A- and B-boxes. Most notably, each DNA-binding element binds to and thus bridges adjacent DNA duplexes. These unique structural features of ParB explain how this protein can bind complex arrays of A- and B-box elements on adjacent DNA arms of the looped partition site.

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