9VLH | pdb_00009vlh

Crystal structure of Bacillus subtilis DegQ tetramer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.254 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.224 (DCC) 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Tetrameric structure of Bacillus subtilis DegQ and its predicted interaction with the DegS-DegU two-component system.

Fujimoto, Z.Kishine, N.Saitou, K.Kimura, K.

(2025) Acta Crystallogr F Struct Biol Commun 81: 425-433

  • DOI: https://doi.org/10.1107/S2053230X25007903
  • Primary Citation of Related Structures:  
    9VLH, 9VLI

  • PubMed Abstract: 

    Bacillus subtilis DegQ is a 46-amino-acid regulatory protein involved in the DegS-DegU two-component system. DegQ promotes the phosphorylation of DegU by DegS, switching the function of DegU from competence to the induction of poly-γ-glutamate production. To elucidate its structural role, we determined the crystal structures of wild-type DegQ and its mutant DegQS25L. Each DegQ monomer folds into a single α-helix, and four monomers assemble into a tetramer characterized by a four-helix coiled-coil structure. Within the tetramer, two adjacent helices are oriented in the same direction, while the other two are oriented oppositely, forming a pseudo-twofold symmetric arrangement. The mutant form displays disrupted symmetry due to altered helix packing, which is caused by shifts in the coiled-coil heptad register induced by the mutation. Structural predictions using AlphaFold3 suggest that DegQ likely binds to the N-terminal helix bundle of DegS, either as a dimer or as individual monomers. These findings provide structural insight into DegQ oligomerization and its potential role in modulating DegS autophosphorylation and DegU binding.


  • Organizational Affiliation
    • Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Degradation enzyme regulation protein DegQ
A, B, C, D, E
A, B, C, D, E, F, G, H
46Bacillus subtilisMutation(s): 0 
Gene Names: degQamyBsacQBSU31720
UniProt
Find proteins for Q99039 (Bacillus subtilis (strain 168))
Explore Q99039 
Go to UniProtKB:  Q99039
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99039
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.254 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.224 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.548α = 87.443
b = 52.271β = 89.567
c = 53.098γ = 89.936
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
Arcimboldophasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release
  • Version 1.1: 2025-10-08
    Changes: Database references