6JIC

Identification and Characterization of a carboxypeptidase inhibitor from Lycium barbarum

• PDB DOI: https://doi.org/10.2210/pdb6JIC/pdb

• Classification: PLANT PROTEIN
• Organism(s): Lycium barbarum
• Mutation(s): No 


• Deposited: 2019-02-20 Released: 2020-02-26 
• Deposition Author(s): Tan, W.L., Wong, K.H., Huang, J.Y., Tay, S.V., Wang, S.J.
• Funding Organization(s): Ministry of Education (Singapore)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Identification and characterization of a wolfberry carboxypeptidase inhibitor from Lycium barbarum.

Huang, J., Wong, K.H., Tan, W.L., Tay, S.V., Wang, S., Tam, J.P.

(2021) Food Chem 351: 129338-129338

• PubMed: 33647700 
• DOI: https://doi.org/10.1016/j.foodchem.2021.129338
• Primary Citation of Related Structures:  
  6JIC


• PubMed Abstract: 
  

  Hyperstable cysteine-rich peptides (CRPs) represent an underexplored superfamily of bioactives in functional foods. An example is wolfberry of the Lycium barbarum family. Previously, we discovered a CRP, designated α-lybatide, from L. barbarum bark. Herein, we report the discovery of β-lybatide, a novel carboxypeptidase inhibitor belonging to a different CRP family from the wolfberry plant. Proteomic and transcriptomic analyses showed that β-lybatide contains 36 amino acids with six cysteine residues. NMR spectroscopy revealed that β-lybatide displays a knottin-like structure that renders it highly resistant to thermal, chemical and enzymatic degradation, conditions important for keeping its structural integrity in gastrointestinal tract. Biochemical assays showed that β-lybatide is a potent carboxypeptidase inhibitor which could contribute to the wolfberry biological activities. Bioinformatics analysis revealed an additional 49 β-lybatide-like plant carboxypeptidase inhibitors. Together, our results show that β-lybatide is the first and the smallest plant-derived hyperstable carboxypeptidase inhibitor discovered from a functional food.

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Organizational Affiliation: 

School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 4.02 kDa 
• Atom Count: 275 
• Modelled Residue Count: 36 
• Deposited Residue Count: 36 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WCI	A	36	Lycium barbarum	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Tan, W.L., Wong, K.H., Huang, J.Y., Tay, S.V., Wang, S.J.

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Funding Organization	Location	Grant Number
Ministry of Education (Singapore)	Singapore	MOE-2016-T3-1-003

Revision History  

• Version 1.0: 2020-02-26
  Type: Initial release
  
• Version 1.1: 2021-03-10
  Changes: Database references
• Version 1.2: 2023-06-14
  Changes: Database references, Other