9H3F image
Deposition Date 2024-10-16
Release Date 2025-08-06
Last Version Date 2025-08-06
Entry Detail
PDB ID:
9H3F
Title:
Cryo-EM structure of YhaM
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.47 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:3'-5' exoribonuclease YhaM
Gene (Uniprot):yhaM
Chain IDs:A, B, C, D, E, F
Chain Length:321
Number of Molecules:6
Biological Source:Bacillus subtilis
Ligand Molecules
Primary Citation

Abstact

Bacteria acquire new traits through the uptake of genetic material from the environment, a process requiring DNA processing. However, the molecular inventory mediating this process is far from being completely understood. Here, we identify YhaM in Bacillus subtilis as a conserved 3'-deoxyribonuclease essential for the uptake and processing of genetic information in the form of single-stranded DNA. Our results show that YhaM assembles into hexamers in the presence of divalent cations, enhancing substrate binding, which is achieved through its conserved oligonucleotide-binding domain. Cells lacking YhaM show a severe defect in the uptake of plasmids and genomic DNA, but the transduction of double-stranded DNA by the phage SPP1 remains unaffected. These findings highlight a critical role of YhaM in single-stranded DNA maturation during natural transformation. Importantly, this function is conserved in various Gram-positive human pathogens such as Staphylococcus aureus, suggesting that it could contribute to the spread of antibiotic resistance.

Legend

Protein

Chemical

Disease

Primary Citation of related structures