Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Predict Membrane 

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.64 kDa 
• Atom Count: 399 
• Modelled Residue Count: 58 
• Deposited Residue Count: 58 
• Unique protein chains: 1

2MWR

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

• PDB DOI: 10.2210/pdb2MWR/pdb
• BMRB: 25352

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Lactobacillus acidophilus
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2014-11-19 Released: 2015-03-04 
• Deposition Author(s): Vederas, J.C., Acedo, J.Z., van Belkum, M.J., Lohans, C.T.

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Experimental Data Snapshot

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

Literature

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

• PubMed: 25681186 
• DOI: 10.1128/AEM.04265-14
• Primary Citation of Related Structures:  
  2MWR


• 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.

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Organizational Affiliation: 

Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acidocin B	A	58	Lactobacillus acidophilus	Mutation(s): 0  Gene Names: acdB, aciA Membrane Entity: Yes
UniProt
Find proteins for Q48499 (Lactobacillus acidophilus) Explore Q48499  Go to UniProtKB:  Q48499

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10000 
• Conformers Submitted: 20 
• Selection Criteria: all calculated structures submitted 
• OLDERADO: 2MWR Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-11-19 
• Released Date: 2015-03-04 
Deposition Author(s): Vederas, J.C., Acedo, J.Z., van Belkum, M.J., Lohans, C.T.

Revision History  

• Version 1.0: 2015-03-04
  Type: Initial release
  
• Version 1.1: 2015-04-15
  Changes: Database references