8DSS

X-ray crystal structure of Geobacillus stearothermophilus ComEA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.232 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-function studies reveal ComEA contains an oligomerization domain essential for transformation in gram-positive bacteria.

Ahmed, I.Hahn, J.Henrickson, A.Khaja, F.T.Demeler, B.Dubnau, D.Neiditch, M.B.

(2022) Nat Commun 13: 7724-7724

  • DOI: https://doi.org/10.1038/s41467-022-35129-0
  • Primary Citation of Related Structures:  
    8DFK, 8DSS

  • PubMed Abstract: 

    An essential step in bacterial transformation is the uptake of DNA into the periplasm, across the thick peptidoglycan cell wall of Gram-positive bacteria, or the outer membrane and thin peptidoglycan layer of Gram-negative bacteria. ComEA, a DNA-binding protein widely conserved in transformable bacteria, is required for this uptake step. Here we determine X-ray crystal structures of ComEA from two Gram-positive species, Bacillus subtilis and Geobacillus stearothermophilus, identifying a domain that is absent in Gram-negative bacteria. X-ray crystallographic, genetic, and analytical ultracentrifugation (AUC) analyses reveal that this domain drives ComEA oligomerization, which we show is required for transformation. We use multi-wavelength AUC (MW-AUC) to characterize the interaction between DNA and the ComEA DNA-binding domain. Finally, we present a model for the interaction of the ComEA DNA-binding domain with DNA, suggesting that ComEA oligomerization may provide a pulling force that drives DNA uptake across the thick cell walls of Gram-positive bacteria.


  • Organizational Affiliation

    Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical Health Sciences, Newark, NJ, 07103, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ComE operon protein 1
A, B
148Geobacillus stearothermophilus ATCC 7953Mutation(s): 0 
Gene Names: B4109_2104B4114_2221D9548_03605GS458_2294TGS27_0901
UniProt
Find proteins for A0A0K9HI54 (Geobacillus stearothermophilus)
Explore A0A0K9HI54 
Go to UniProtKB:  A0A0K9HI54
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K9HI54
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.232 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.706α = 90
b = 80.706β = 90
c = 71.279γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM057720

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description