Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3.26 kDa 
• Atom Count: 223 
• Modelled Residue Count: 32 
• Deposited Residue Count: 32 
• Unique protein chains: 1

2KTN

Spatial structure of Lch-alpha peptide from two-component lantibiotic system Lichenicidin VK21

• PDB DOI: 10.2210/pdb2KTN/pdb
• BMRB: 16709

• Classification: ANTIBIOTIC
• Organism(s): Bacillus licheniformis DSM 13 = ATCC 14580
• Mutation(s): No 


• Deposited: 2010-02-05 Released: 2010-07-21 
• Deposition Author(s): Mineev, K.S., Shenkarev, Z.O., Ovchinnikova, T.V., Arseniev, A.S.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Isolation, Structure Elucidation, and Synergistic Antibacterial Activity of a Novel Two-Component Lantibiotic Lichenicidin from Bacillus Licheniformis Vk21.

Shenkarev, Z.O., Finkina, E.I., Nurmukhamedova, E.K., Balandin, S.V., Mineev, K.S., Nadezhdin, K.D., Yakimenko, Z.A., Tagaev, A.A., Temirov, Y.V., Arseniev, A.S., Ovchinnikova, T.V.

(2010) Biochemistry 49: 6462

• PubMed: 20578714 
• DOI: 10.1021/bi100871b
• Primary Citation of Related Structures:  
  2KTN, 2KTO


• PubMed Abstract: 
  

A novel synergetic lantibiotic pair, Lchalpha (3249.51 Da) and Lchbeta (3019.36 Da), termed lichenicidin VK21, was isolated from the producer strain Bacillus licheniformis VK21. Chemical and spatial structures of Lchalpha and Lchbeta were determined. Each peptide contains 31 amino acid residues linked by 4 intramolecular thioether bridges and the N-terminal 2-oxobutyryl group. Spatial structures of Lchalpha and Lchbeta were studied by NMR spectroscopy in methanol solution. The Lchalpha peptide displays structural homology with mersacidin-like lantibiotics and involves relatively well-structured N- and C-terminal domains connected by a flexible loop stabilized by a thioether bridge Ala11-S-Ala21. In contrast, the Lchbeta peptide represents a prolonged hydrophobic alpha-helix flanked with more flexible N- and C-terminal domains. A lantibiotic cluster of the Bacillus licheniformis VK21 genome which comprises the structural genes, lchA1 and lchA2, encoding the lantibiotics precursors, as well as the gene of a modifying enzyme lchM1, was amplified and sequenced. The mature peptides, Lchalpha and Lchbeta, interact synergistically to possess antibiotic activity against Gram-positive bacteria within a nanomolar concentration range, though the individual peptides were shown to be active at micromolar concentrations. Our results afford molecular insight into the mechanism of lichenicidin VK21 action.

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Organizational Affiliation: 

Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str. 16/10, Moscow, Russia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LICHENICIDIN VK21 A1	A	32	Bacillus licheniformis DSM 13 = ATCC 14580	Mutation(s): 0
UniProt
Find proteins for P86475 (Bacillus licheniformis) Explore P86475  Go to UniProtKB:  P86475

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DBU	A	PEPTIDE LINKING	C4 H7 N O2		THR
DHA	A	PEPTIDE LINKING	C3 H5 N O2		SER

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000197	A	ALPHA LICHENICIDIN PREPEPTIDE	Polypeptide / Antibiotic		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: target function 
• OLDERADO: 2KTN Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-05 
• Released Date: 2010-07-21 
Deposition Author(s): Mineev, K.S., Shenkarev, Z.O., Ovchinnikova, T.V., Arseniev, A.S.

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-06-14
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-07-27
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 1.4: 2011-08-10
  Changes: Other
• Version 1.5: 2012-12-12
  Changes: Other