2MP8 | pdb_00002mp8

NMR structure of NKR-5-3B

• PDB DOI: https://doi.org/10.2210/pdb2MP8/pdb
• BMRB: 19970

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Enterococcus faecalis
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2014-05-13 Released: 2015-05-13 
• Deposition Author(s): Rosengren, K.J., Craik, D.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Identification, Characterization, and Three-Dimensional Structure of the Novel Circular Bacteriocin, Enterocin NKR-5-3B, from Enterococcus faecium

Himeno, K., Rosengren, K.J., Inoue, T., Perez, R.H., Colgrave, M.L., Lee, H.S., Chan, L.Y., Henriques, S.T., Fujita, K., Ishibashi, N., Zendo, T., Wilaipun, P., Nakayama, J., Leelawatcharamas, V., Jikuya, H., Craik, D.J., Sonomoto, K.

(2015) Biochemistry 54: 4863-4876

• PubMed: 26174911 
• DOI: https://doi.org/10.1021/acs.biochem.5b00196
• Primary Citation Related Structures: 
  2MP8


• PubMed Abstract: 
  

  Enterocin NKR-5-3B, one of the multiple bacteriocins produced by Enterococcus faecium NKR-5-3, is a 64-amino acid novel circular bacteriocin that displays broad-spectrum antimicrobial activity. Here we report the identification, characterization, and three-dimensional nuclear magnetic resonance solution structure determination of enterocin NKR-5-3B. Enterocin NKR-5-3B is characterized by four helical segments that enclose a compact hydrophobic core, which together with its circular backbone impart high stability and structural integrity. We also report the corresponding structural gene, enkB, that encodes an 87-amino acid precursor peptide that undergoes a yet to be described enzymatic processing that involves adjacent cleavage and ligation of Leu(24) and Trp(87) to yield the mature (circular) enterocin NKR-5-3B.

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Organizational Affiliation: 
• †Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
⊥Department of Fishery Products, Faculty of Fisheries, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.
@Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Chatuchak, Bangkok 10900, Thailand.
#Department of Functional Metabolic Design, Bio-Architecture Center, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.34 kDa 
• Atom Count: 446 
• Modeled Residue Count: 64 
• Deposited Residue Count: 64 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NKR-5-3B	A	64	Enterococcus faecalis	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A0M3KKS4 (Enterococcus faecalis) Explore A0A0M3KKS4  Go to UniProtKB:  A0A0M3KKS4

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-13 
Deposition Author(s): Rosengren, K.J., Craik, D.J.

Revision History  

• Version 1.0: 2015-05-13
  Type: Initial release
  
• Version 1.1: 2016-06-01
  Changes: Database references
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary