Crystal Structure of the GerD spore germination protein

Experimental Data Snapshot

  • Resolution: 2.29 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

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Structural and Functional Analysis of the GerD Spore Germination Protein of Bacillus Species.

Li, Y.Jin, K.Ghosh, S.Devarakonda, P.Carlson, K.Davis, A.Stewart, K.A.Cammett, E.Rossi, P.P.Setlow, B.Lu, M.Setlow, P.Hao, B.

(2014) J Mol Biol 426: 1995-2008

  • DOI: https://doi.org/10.1016/j.jmb.2014.02.004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Spore germination in Bacillus species represents an excellent model system with which to study the molecular mechanisms underlying the nutritional control of growth and development. Binding of specific chemical nutrients to their cognate receptors located in the spore inner membrane triggers the germination process that leads to a resumption of metabolism in spore outgrowth. Recent studies suggest that the inner membrane GerD lipoprotein plays a critical role in the receptor-mediated activation of downstream germination events. The 121-residue core polypeptide of GerD (GerD⁶⁰⁻¹⁸⁰) from Geobacillus stearothermophilus forms a stable α-helical trimer in aqueous solution. The 2.3-Å-resolution crystal structure of the trimer reveals a neatly twisted superhelical rope, with unusual supercoiling induced by parallel triple-helix interactions. The overall geometry comprises three interleaved hydrophobic screws of interacting helices linked by short turns that have not been seen before. Using complementation analysis in a series of Bacillus subtilis gerD mutants, we demonstrated that alterations in the GerD trimer structure have profound effects on nutrient germination. This important structure-function relationship of trimeric GerD is supported by our identification of a dominant negative gerD mutation in B. subtilis. These results and those of others lead us to propose that GerD mediates clustering of germination proteins in the inner membrane of dormant spores and thus promotes the rapid and cooperative germination response to nutrients.

  • Organizational Affiliation

    Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030-3305, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spore germination protein
A, B, C, D, E
A, B, C, D, E, F
125Geobacillus kaustophilus HTA426Mutation(s): 1 
Gene Names: gerDGK0144
Find proteins for Q5L3Q1 (Geobacillus kaustophilus (strain HTA426))
Explore Q5L3Q1 
Go to UniProtKB:  Q5L3Q1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5L3Q1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.29 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.748α = 90
b = 98.45β = 90
c = 127.485γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-04-23
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references