Solution Structure of Acidocin B, a Circular Bacteriocin from Lactobacillus acidophilus M46

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 10000 
  • Conformers Submitted: 20 
  • Selection Criteria: all calculated structures submitted 

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Solution Structure of Acidocin B, a Circular Bacteriocin Produced by Lactobacillus acidophilus M46.

Acedo, J.Z.van Belkum, M.J.Lohans, C.T.McKay, R.T.Miskolzie, M.Vederas, J.C.

(2015) Appl Environ Microbiol 81: 2910-2918

  • DOI: https://doi.org/10.1128/AEM.04265-14
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Acidocin B, a bacteriocin produced by Lactobacillus acidophilus M46, was originally reported to be a linear peptide composed of 59 amino acid residues. However, its high sequence similarity to gassericin A, a circular bacteriocin from Lactobacillus gasseri LA39, suggested that acidocin B might be circular as well. Acidocin B was purified from culture supernatant by a series of hydrophobic interaction chromatographic steps. Its circular nature was ascertained by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and tandem mass spectrometry (MS/MS) sequencing. The peptide sequence was found to consist of 58 amino acids with a molecular mass of 5,621.5 Da. The sequence of the acidocin B biosynthetic gene cluster was also determined and showed high nucleotide sequence similarity to that of gassericin A. The nuclear magnetic resonance (NMR) solution structure of acidocin B in sodium dodecyl sulfate micelles was elucidated, revealing that it is composed of four α-helices of similar length that are folded to form a compact, globular bundle with a central pore. This is a three-dimensional structure for a member of subgroup II circular bacteriocins, which are classified based on their isoelectric points of ∼7 or lower. Comparison of acidocin B with carnocyclin A, a subgroup I circular bacteriocin with four α-helices and a pI of 10, revealed differences in the overall folding. The observed variations could be attributed to inherent diversity in their physical properties, which also required the use of different solvent systems for three-dimensional structural elucidation.

  • Organizational Affiliation

    Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acidocin B58Lactobacillus acidophilusMutation(s): 0 
Membrane Entity: Yes 
Find proteins for Q48499 (Lactobacillus acidophilus)
Explore Q48499 
Go to UniProtKB:  Q48499
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UniProt GroupQ48499
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 10000 
  • Conformers Submitted: 20 
  • Selection Criteria: all calculated structures submitted 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Database references, Derived calculations, Other