3MKZ

Structure of SopB(155-272)-18mer complex, P21 form

Summary for 3MKZ

• Entry DOI: 10.2210/pdb3mkz/pdb
• Related: 3MKW 3MKY
• Descriptor: Protein sopB, DNA (5'-D(*CP*TP*GP*GP*GP*AP*CP*CP*AP*TP*GP*GP*TP*CP*CP*CP*AP*G)-3'), CALCIUM ION, ... (4 entities in total)
• Functional Keywords: partition, sopb, f plasmid, centromere, dna-binding protein-dna complex, dna-binding protein/dna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 8
• Total formula weight: 75302.30

Authors

Schumacher, M.A. (deposition date: 2010-04-15, release date: 2010-05-05, Last modification date: 2023-09-06)

Primary citation

Schumacher, M.A.,Piro, K.M.,Xu, W.
Insight into F plasmid DNA segregation revealed by structures of SopB and SopB-DNA complexes.
Nucleic Acids Res., 38:4514-4526, 2010

PubMed Abstract: Accurate DNA segregation is essential for genome transmission. Segregation of the prototypical F plasmid requires the centromere-binding protein SopB, the NTPase SopA and the sopC centromere. SopB displays an intriguing range of DNA-binding properties essential for partition; it binds sopC to form a partition complex, which recruits SopA, and it also coats DNA to prevent non-specific SopA-DNA interactions, which inhibits SopA polymerization. To understand the myriad functions of SopB, we determined a series of SopB-DNA crystal structures. SopB does not distort its DNA site and our data suggest that SopB-sopC forms an extended rather than wrapped partition complex with the SopA-interacting domains aligned on one face. SopB is a multidomain protein, which like P1 ParB contains an all-helical DNA-binding domain that is flexibly attached to a compact (beta(3)-alpha)(2) dimer-domain. Unlike P1 ParB, the SopB dimer-domain does not bind DNA. Moreover, SopB contains a unique secondary dimerization motif that bridges between DNA duplexes. Both specific and non-specific SopB-DNA bridging structures were observed. This DNA-linking function suggests a novel mechanism for in trans DNA spreading by SopB, explaining how it might mask DNA to prevent DNA-mediated inhibition of SopA polymerization.

PubMed: 20236989
DOI: 10.1093/nar/gkq161

Experimental method

X-RAY DIFFRACTION (2.98 Å)