The CTP-binding domain is disengaged from the DNA-binding domain in a cocrystal structure of Bacillus subtilis Noc–DNA complex

Journal of Biological ChemistryJournal of Biological ChemistryVolume 299, Issue 4, April 2023, 103063Journal home page for Journal of Biological ChemistryAuthor links open overlay panel, , , , ,

In Bacillus subtilis, a ParB-like nucleoid occlusion protein (Noc) binds specifically to Noc-binding sites (NBSs) on the chromosome to help coordinate chromosome segregation and cell division. Noc does so by binding to CTP to form large membrane-associated nucleoprotein complexes to physically inhibit the assembly of the cell division machinery. The site-specific binding of Noc to NBS DNA is a prerequisite for CTP-binding and the subsequent formation of a membrane-active DNA-entrapped protein complex. Here, we solve the structure of a C-terminally truncated B. subtilis Noc bound to NBS DNA to reveal the conformation of Noc at this crucial step. Our structure reveals the disengagement between the N-terminal CTP-binding domain and the NBS-binding domain of each DNA-bound Noc subunit; this is driven, in part, by the swapping of helices 4 and 5 at the interface of the two domains. Site-specific crosslinking data suggest that this conformation of Noc-NBS exists in solution. Overall, our results lend support to the recent proposal that parS/NBS binding catalyzes CTP binding and DNA entrapment by preventing the reengagement of the CTP-binding domain and the DNA-binding domain from the same ParB/Noc subunit.

Keywords

ParB

Noc

CTP

cell division

DNA-binding proteins

X-ray crystallography

chromosome

microbiology

AbbreviationsHDX-MS

Hydrogen-deuterium exchange coupled to mass spectrometry

InterXL

Intermolecular singly crosslinked species

Inter2XL

Intermolecular doubly crosslinked species

IntraXL

Intramolecular crosslinked species

Noc

Nucleoid occlusion protein

ParB

Partitioning protein B

parS

Partitioning protein B–binding site

© 2023 THE AUTHORS. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology.

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