9H3F

Cryo-EM structure of YhaM

Summary for 9H3F

• Entry DOI: 10.2210/pdb9h3f/pdb
• EMDB information: 51819
• Descriptor: 3'-5' exoribonuclease YhaM, MAGNESIUM ION (2 entities in total)
• Functional Keywords: 3'-5' exoribonuclease, dna binding protein
• Biological source: Bacillus subtilis
• Total number of polymer chains: 6
• Total formula weight: 219999.22

Authors

Pane-Farre, J.,Madej, M.G.,Fu, L.,Ziegler, C.,Hinrichs, R. (deposition date: 2024-10-16, release date: 2025-08-06)

Primary citation

Hanssmann, J.,Pane-Farre, J.,Meiser, M.,Girbig, M.,Fu, L.,Madej, M.G.,Sendker, F.L.,Tholken, C.,Lechner, M.,Ziegler, C.,Hochberg, G.K.A.,Bange, G.,Thanbichler, M.,Hinrichs, R.
A conserved nuclease facilitates environmental DNA uptake.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: 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.

PubMed: 40421801
DOI: 10.1093/nar/gkaf443

Experimental method

ELECTRON MICROSCOPY (3.47 Å)