Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.25 kDa 
• Atom Count: 361 
• Modelled Residue Count: 43 
• Deposited Residue Count: 43 
• Unique protein chains: 1

2KUY

Structure of Glycocin F

• PDB DOI: 10.2210/pdb2KUY/pdb
• BMRB: 16747

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Lactiplantibacillus plantarum
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2010-03-01 Released: 2011-05-04 
• Deposition Author(s): Venugopal, H., Edwards, P., Schwalbe, M., Claridge, J., Stepper, J., Patchett, M., Loo, T., Libich, D., Norris, G., Pascal, S.

---

Experimental Data Snapshot

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

Literature

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

• PubMed: 21395300 
• DOI: 10.1021/bi200217u
• Primary Citation of Related Structures:  
  2KUY


• 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. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prebacteriocin glycocin F	A	43	Lactiplantibacillus plantarum	Mutation(s): 0  Gene Names: gccF Membrane Entity: Yes
UniProt
Find proteins for E9K9Z1 (Lactiplantibacillus plantarum) Explore E9K9Z1  Go to UniProtKB:  E9K9Z1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 12 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2KUY Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-03-01 
• Released Date: 2011-05-04 
Deposition Author(s): Venugopal, H., Edwards, P., Schwalbe, M., Claridge, J., Stepper, J., Patchett, M., Loo, T., Libich, D., Norris, G., Pascal, S.

Revision History  

• 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