9H3F | pdb_00009h3f

Cryo-EM structure of YhaM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A conserved nuclease facilitates environmental DNA uptake.

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.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkaf443
  • Primary Citation of Related Structures:  
    9H3F

  • 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.


  • Organizational Affiliation
    • Department of Biology, University of Marburg, 35043 Marburg, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3'-5' exoribonuclease YhaM
A, B, C, D, E
A, B, C, D, E, F
321Bacillus subtilisMutation(s): 0 
Gene Names: yhaMBSU09930
EC: 3.1
UniProt
Find proteins for O07521 (Bacillus subtilis (strain 168))
Explore O07521 
Go to UniProtKB:  O07521
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO07521
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth B]
J [auth B]
K [auth C]
G [auth A],
H [auth A],
I [auth B],
J [auth B],
K [auth C],
L [auth C],
M [auth D],
N [auth D],
O [auth E],
P [auth E],
Q [auth F],
R [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentSYN/5/2023

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release