8ULM | pdb_00008ulm

Chickpea (Cicer arientinum) nodule-specific cysteine-rich peptide NCR13: Solution NMR structure of the isomer with C4:C23, C15:C30, and C10:C28 disulfide bonds


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Chickpea NCR13 disulfide cross-linking variants exhibit profound differences in antifungal activity and modes of action.

Godwin, J.Djami-Tchatchou, A.T.Velivelli, S.L.S.Tetorya, M.Kalunke, R.Pokhrel, A.Zhou, M.Buchko, G.W.Czymmek, K.J.Shah, D.M.

(2024) PLoS Pathog 20: e1012745-e1012745

  • DOI: https://doi.org/10.1371/journal.ppat.1012745
  • Primary Citation of Related Structures:  
    7TH8, 8ULM

  • PubMed Abstract: 

    Small cysteine-rich antifungal peptides with multi-site modes of action (MoA) have potential for development as biofungicides. In particular, legumes of the inverted repeat-lacking clade express a large family of nodule-specific cysteine-rich (NCR) peptides that orchestrate differentiation of nitrogen-fixing bacteria into bacteroids. These NCRs can form two or three intramolecular disulfide bonds and a subset of these peptides with high cationicity exhibits antifungal activity. However, the importance of intramolecular disulfide pairing and MoA against fungal pathogens for most of these plant peptides remains to be elucidated. Our study focused on a highly cationic chickpea NCR13, which has a net charge of +8 and contains six cysteines capable of forming three disulfide bonds. NCR13 expression in Pichia pastoris resulted in formation of two peptide folding variants, NCR13_PFV1 and NCR13_PFV2, that differed in the pairing of two out of three disulfide bonds despite having an identical amino acid sequence. The NMR structure of each PFV revealed a unique three-dimensional fold with the PFV1 structure being more compact but less dynamic. Surprisingly, PFV1 and PFV2 differed profoundly in the potency of antifungal activity against several fungal plant pathogens and their multi-faceted MoA. PFV1 showed significantly faster fungal cell-permeabilizing and cell entry capabilities as well as greater stability once inside the fungal cells. Additionally, PFV1 was more effective in binding fungal ribosomal RNA and inhibiting protein translation in vitro. Furthermore, when sprayed on pepper and tomato plants, PFV1 was more effective in reducing disease symptoms caused by Botrytis cinerea, causal agent of gray mold disease in fruits, vegetables, and flowers. In conclusion, our work highlights the significant impact of disulfide pairing on the antifungal activity and MoA of NCR13 and provides a structural framework for design of novel, potent antifungal peptides for agricultural use.


  • Organizational Affiliation
    • Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nodule cysteine-rich protein 1333Cicer arietinumMutation(s): 0 
Gene Names: NCR13
UniProt
Find proteins for A0A0U8SNQ0 (Cicer arietinum)
Explore A0A0U8SNQ0 
Go to UniProtKB:  A0A0U8SNQ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U8SNQ0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Database references, Structure summary
  • Version 1.2: 2024-12-25
    Changes: Database references