3NO7

Crystal structure of the centromere-binding protein ParB from plasmid pCXC100

Summary for 3NO7

• Entry DOI: 10.2210/pdb3no7/pdb
• Descriptor: Putative plasmid related protein, SULFATE ION (3 entities in total)
• Functional Keywords: ribbon-helix-helix, dna binding protein
• Biological source: Leifsonia xyli subsp. cynodontis (Clavibacter xyli cynodontis)
• Total number of polymer chains: 2
• Total formula weight: 18998.69

Authors

Ye, K. (deposition date: 2010-06-24, release date: 2010-12-22, Last modification date: 2023-12-27)

Primary citation

Huang, L.,Yin, P.,Zhu, X.,Zhang, Y.,Ye, K.
Crystal structure and centromere binding of the plasmid segregation protein ParB from pCXC100
Nucleic Acids Res., 39:2954-2968, 2011

PubMed Abstract: Plasmid pCXC100 from the Gram-positive bacterium Leifsonia xyli subsp. cynodontis uses a type Ib partition system that includes a centromere region, a Walker-type ATPase ParA and a centromere-binding protein ParB for stable segregation. However, ParB shows no detectable sequence homology to any DNA-binding motif. Here, we study the ParB centromere interaction by structural and biochemical approaches. The crystal structure of the C-terminal DNA-binding domain of ParB at 1.4 Å resolution reveals a dimeric ribbon-helix-helix (RHH) motif, supporting the prevalence of RHH motif in centromere binding. Using hydroxyl radical footprinting and quantitative binding assays, we show that the centromere core comprises nine uninterrupted 9-nt direct repeats that can be successively bound by ParB dimers in a cooperative manner. However, the interaction of ParB with a single subsite requires 18 base pairs covering one immediate repeat as well as two halves of flanking repeats. Through mutagenesis, sequence specificity was determined for each position of an 18-bp subsite. These data suggest an unique centromere recognition mechanism by which the repeat sequence is jointly specified by adjacent ParB dimers bound to an overlapped region.

PubMed: 21123191
DOI: 10.1093/nar/gkq915

Experimental method

X-RAY DIFFRACTION (1.4 Å)