Bacillus subtilis phosphoglucomutase GlmM (phosphate bound)

Experimental Data Snapshot

  • Resolution: 3.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

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Structural basis for the inhibition of the Bacillus subtilis c-di-AMP cyclase CdaA by the phosphoglucomutase GlmM.

Pathania, M.Tosi, T.Millership, C.Hoshiga, F.Morgan, R.M.L.Freemont, P.S.Grundling, A.

(2021) J Biol Chem 297: 101317-101317

  • DOI: https://doi.org/10.1016/j.jbc.2021.101317
  • Primary Citation of Related Structures:  
    7OJR, 7OJS, 7OLH, 7OML

  • PubMed Abstract: 

    Cyclic-di-adenosine monophosphate (c-di-AMP) is an important nucleotide signaling molecule that plays a key role in osmotic regulation in bacteria. c-di-AMP is produced from two molecules of ATP by proteins containing a diadenylate cyclase (DAC) domain. In Bacillus subtilis, the main c-di-AMP cyclase, CdaA, is a membrane-linked cyclase with an N-terminal transmembrane domain followed by the cytoplasmic DAC domain. As both high and low levels of c-di-AMP have a negative impact on bacterial growth, the cellular levels of this signaling nucleotide are tightly regulated. Here we investigated how the activity of the B. subtilis CdaA is regulated by the phosphoglucomutase GlmM, which has been shown to interact with the c-di-AMP cyclase. Using the soluble B. subtilis CdaA CD catalytic domain and purified full-length GlmM or the GlmM F369 variant lacking the C-terminal flexible domain 4, we show that the cyclase and phosphoglucomutase form a stable complex in vitro and that GlmM is a potent cyclase inhibitor. We determined the crystal structure of the individual B. subtilis CdaA CD and GlmM homodimers and of the CdaA CD :GlmM F369 complex. In the complex structure, a CdaA CD dimer is bound to a GlmM F369 dimer in such a manner that GlmM blocks the oligomerization of CdaA CD and formation of active head-to-head cyclase oligomers, thus suggesting a mechanism by which GlmM acts as a cyclase inhibitor. As the amino acids at the CdaA CD :GlmM interphase are conserved, we propose that the observed mechanism of inhibition of CdaA by GlmM may also be conserved among Firmicutes.

  • Organizational Affiliation

    Section of Molecular Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglucosamine mutase464Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: glmMybbTBSU01770
Find proteins for O34824 (Bacillus subtilis (strain 168))
Explore O34824 
Go to UniProtKB:  O34824
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34824
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on PO4

Download Ideal Coordinates CCD File 
O4 P
Experimental Data & Validation

Experimental Data

  • Resolution: 3.05 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.876α = 90
b = 134.876β = 90
c = 69.18γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
xia2data reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomP63775

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-27
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description