9F0E image
Entry Detail
PDB ID:
9F0E
Title:
Bacterial histone protein HBb from Bdellovibrio bacteriovorus bound to DNA
Biological Source:
PDB Version:
Deposition Date:
2024-04-15
Release Date:
2024-06-26
Method Details:
Experimental Method:
Resolution:
1.85 Å
R-Value Free:
0.26
R-Value Work:
0.24
R-Value Observed:
0.24
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Transcription factor CBF/NF-Y/archaeal histone domain-containing protein
Chain IDs:A, B
Chain Length:66
Number of Molecules:2
Biological Source:Bdellovibrio bacteriovorus HD100
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*CP*GP*TP*TP*AP*AP*AP*GP*C)-3')
Chain IDs:C
Chain Length:20
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
Primary Citation
Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending.
Nucleic Acids Res. 52 8193 8204 (2024)
PMID: 38864377 DOI: 10.1093/nar/gkae485

Abstact

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.

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Primary Citation of related structures