9OIL | pdb_00009oil

Solution Structure of the Broadspectrum Bacteriocin Garvicin Q

• PDB DOI: https://doi.org/10.2210/pdb9OIL/pdb
• BMRB: 53020

• Classification: ANTIBIOTIC
• Organism(s): Lactococcus garvieae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-05-06 Released: 2025-08-20 
• Deposition Author(s): Mallett, T.M., Lamer, T., Aleksandrzak-Piekarczyk, T., Mckay, R.T., Sit, C.S., Rainey, J.K., Van Belkum, M., Vederas, J.C.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 1000 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Solution Structure of the Broad-Spectrum Bacteriocin Garvicin Q.

Mallett, T., Lamer, T., Aleksandrzak-Piekarczyk, T., McKay, R.T., Catenza, K., Sit, C., Rainey, J.K., Towle-Straub, K.M., Vederas, J.C., van Belkum, M.J.

(2025) Int J Mol Sci 26

• PubMed: 40869166 
• DOI: https://doi.org/10.3390/ijms26167846
• Primary Citation Related Structures: 
  9OIL, 9OIU


• PubMed Abstract: 
  

  Class IId bacteriocins are linear, unmodified antimicrobial peptides produced by Gram-positive bacteria, and often display potent, narrow-spectrum inhibition spectra. Garvicin Q (GarQ) is a class IId bacteriocin produced by the lactic acid bacterium Lactococcus garvieae . It stands out for its unusual broad-spectrum antimicrobial activity against various bacterial species, including Listeria monocytogenes , Pediococcus pentosaceus , Carnobacterium maltaromaticum , Enterococcus faecalis , and Lactococcus spp. Its protein target is the mannose phosphotransferase system (Man-PTS) of susceptible bacterial strains, though little is known about the precise molecular mechanism behind GarQ's unusual broad spectrum of activity. In this work, ¹³ C- and ¹⁵ N-labelled GarQ was recombinantly produced using our previously described "sandwiched" protein expression system in Escherichia coli . We also developed a protocol to purify a uniformly labelled sample of the small ubiquitin-like modifier His ₆ -SUMO, which is produced as a byproduct of the expression procedure. We demonstrated its use as a "free" protein standard for 3D NMR experiment calibrations. The GarQ solution structure was solved using triple-resonance nuclear magnetic resonance (NMR) spectroscopy and was compared with the structures of other Man-PTS-targeting bacteriocins. GarQ adopts a helix-hinge-helix fold, which is contrary to its structural predictions according to AlphaFold 3.

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Organizational Affiliation: 
• Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.
Department of Chemistry, Saint Mary's University, Halifax, NS B3H 3C3, Canada.
Department of Biochemistry & Molecular Biology, Department of Chemistry, School of Biomedical Engineering, Dalhousie University, Halifax, NS B3H 4R2, Canada.
Department of Physical Sciences, MacEwan University, Edmonton, AB T5J 2P2, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 5.35 kDa 
• Atom Count: 379 
• Modeled Residue Count: 50 
• Deposited Residue Count: 50 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prepeptide GarQ	A	50	Lactococcus garvieae	Mutation(s): 0  Gene Names: garQ
UniProt
Find proteins for H6U5Y1 (Lactococcus garvieae) Explore H6U5Y1  Go to UniProtKB:  H6U5Y1

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 1000 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Mallett, T.M., Lamer, T., Aleksandrzak-Piekarczyk, T., Mckay, R.T., Sit, C.S., Rainey, J.K., Van Belkum, M., Vederas, J.C.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release
  
• Version 1.1: 2025-09-10
  Changes: Database references