9F0E

Bacterial histone protein HBb from Bdellovibrio bacteriovorus bound to DNA

Summary for 9F0E

• Entry DOI: 10.2210/pdb9f0e/pdb
• Related: 8CMP 9EZZ
• Descriptor: Transcription factor CBF/NF-Y/archaeal histone domain-containing protein, DNA (5'-D(P*CP*GP*TP*TP*AP*AP*AP*GP*C)-3'), PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: bacterial histone, protein-dna complex, dna binding protein
• Biological source: Bdellovibrio bacteriovorus HD100; More
• Total number of polymer chains: 3
• Total formula weight: 20766.89

Authors

Hu, Y.,Albrecht, R.,Hartmann, M.D. (deposition date: 2024-04-15, release date: 2024-06-26, Last modification date: 2024-10-09)

Primary citation

Hu, Y.,Schwab, S.,Deiss, S.,Escudeiro, P.,van Heesch, T.,Joiner, J.D.,Vreede, J.,Hartmann, M.D.,Lupas, A.N.,Alvarez, B.H.,Alva, V.,Dame, R.T.
Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending.
Nucleic Acids Res., 52:8193-8204, 2024

PubMed Abstract: Histones are essential for genome compaction and transcription regulation in eukaryotes, where they assemble into octamers to form the nucleosome core. In contrast, archaeal histones assemble into dimers that form hypernucleosomes upon DNA binding. Although histone homologs have been identified in bacteria recently, their DNA-binding characteristics remain largely unexplored. Our study reveals that the bacterial histone HBb (Bd0055) is indispensable for the survival of Bdellovibrio bacteriovorus, suggesting critical roles in DNA organization and gene regulation. By determining crystal structures of free and DNA-bound HBb, we unveil its distinctive dimeric assembly, diverging from those of eukaryotic and archaeal histones, while also elucidating how it binds and bends DNA through interaction interfaces reminiscent of eukaryotic and archaeal histones. Building on this, by employing various biophysical and biochemical approaches, we further substantiated the ability of HBb to bind and compact DNA by bending in a sequence-independent manner. Finally, using DNA affinity purification and sequencing, we reveal that HBb binds along the entire genomic DNA of B. bacteriovorus without sequence specificity. These distinct DNA-binding properties of bacterial histones, showcasing remarkable similarities yet significant differences from their archaeal and eukaryotic counterparts, highlight the diverse roles histones play in DNA organization across all domains of life.

PubMed: 38864377
DOI: 10.1093/nar/gkae485

Experimental method

X-RAY DIFFRACTION (1.85 Å)