Structure of Glycocin F

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 12 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Structural, dynamic, and chemical characterization of a novel s-glycosylated bacteriocin.

Venugopal, H.Edwards, P.J.Schwalbe, M.Claridge, J.K.Libich, D.S.Stepper, J.Loo, T.Patchett, M.L.Norris, G.E.Pascal, S.M.

(2011) Biochemistry 50: 2748-2755

  • DOI: https://doi.org/10.1021/bi200217u
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Bacteriocins are bacterial peptides with specific activity against competing species. They hold great potential as natural preservatives and for their probiotic effects. We show here nuclear magnetic resonance-based evidence that glycocin F, a 43-amino acid bacteriocin from Lactobacillus plantarum, contains two β-linked N-acetylglucosamine moieties, attached via side chain linkages to a serine via oxygen, and to a cysteine via sulfur. The latter linkage is novel and has helped to establish a new type of post-translational modification, the S-linked sugar. The peptide conformation consists primarily of two α-helices held together by a pair of nested disulfide bonds. The serine-linked sugar is positioned on a short loop sequentially connecting the two helices, while the cysteine-linked sugar presents at the end of a long disordered C-terminal tail. The differing chemical and conformational stabilities of the two N-actetylglucosamine moieties provide clues about the possible mode of action of this bacteriostatic peptide.

  • Organizational Affiliation

    Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand. h.venugopal@massey.ac.nz

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Prebacteriocin glycocin F43Lactiplantibacillus plantarumMutation(s): 0 
Membrane Entity: Yes 
Find proteins for E9K9Z1 (Lactiplantibacillus plantarum)
Explore E9K9Z1 
Go to UniProtKB:  E9K9Z1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE9K9Z1
Glycosylation Sites: 2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
C8 H15 N O6
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 12 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-02-05
    Changes: Data collection, Derived calculations, Other
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-06-14
    Changes: Database references, Other, Structure summary