9EFD

Crystal Structure in space group C2221 of a nucleoid-associated protein (UBP) from Sulfolobus islandicus.

Summary for 9EFD

• Entry DOI: 10.2210/pdb9efd/pdb
• Descriptor: Plasmid pARN4, DI(HYDROXYETHYL)ETHER, TETRAETHYLENE GLYCOL, ... (4 entities in total)
• Functional Keywords: sulfolobus islandicus, archaea, dna sequence specific binding protein, nucleoid-associated protein, dna replication origin binding protein, dna major groove binding protein, dna binding protein
• Biological source: Sulfolobus islandicus REY15A
• Total number of polymer chains: 2
• Total formula weight: 27382.43

Authors

Dhanaraju, R.,Gonzalez-Gutierrez, G.,Bell, S.D. (deposition date: 2024-11-20, release date: 2025-06-11, Last modification date: 2025-06-18)

Primary citation

Dhanaraju, R.,Samson, R.Y.,Feng, X.,Costa, A.,Gonzalez-Gutierrez, G.,Bell, S.D.
An archaeal nucleoid-associated protein binds an essential motif in DNA replication origins.
Nat Commun, 16:5230-5230, 2025

PubMed Abstract: DNA replication typically has defined start sites, or replication origins, which are designated by their recognition by specific initiator proteins. In addition to initiators, general chromatin or nucleoid-associated proteins have been shown to play roles in modulating origin efficiency in eukaryotes and bacteria. The role of chromatin proteins in origin function in the archaeal domain of life is poorly understood. Here, we describe a dissection of sequences elements required for in vivo function of an archaeal DNA replication origin. Our data reveal a hitherto uncharacterized sequence element, the ucm, is required for origin activity. We identify a protein, UBP, that interacts with the ucm and additionally with hundreds of other sites on the genome. We solve the crystal structure of UBP alone and in complex with ucm DNA, and further show that UBP interacts with the MCM replicative helicase. Taken together, our data provide evidence that UBP functions as a general nucleoid-associated protein that plays a key role in facilitating the egress of the MCM replicative helicase from DNA replication origins.

PubMed: 40473630
DOI: 10.1038/s41467-025-60618-3

Experimental method

X-RAY DIFFRACTION (2.74 Å)