6O3Q

NMR solution structure of vicilin-buried peptide-8 (VBP-8)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with acceptable covalent geometry 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An Ancient Peptide Family Buried within Vicilin Precursors.

Zhang, J.Payne, C.D.Pouvreau, B.Schaefer, H.Fisher, M.F.Taylor, N.L.Berkowitz, O.Whelan, J.Rosengren, K.J.Mylne, J.S.

(2019) ACS Chem Biol 14: 979-993

  • DOI: 10.1021/acschembio.9b00167
  • Primary Citation of Related Structures:  
    6O3S, 6O3Q

  • PubMed Abstract: 
  • New proteins can evolve by duplication and divergence or de novo, from previously noncoding DNA. A recently observed mechanism is for peptides to evolve within a "host" protein and emerge by proteolytic processing. The first examples of such interstitial peptides were ones hosted by precursors for seed storage albumin ...

    New proteins can evolve by duplication and divergence or de novo, from previously noncoding DNA. A recently observed mechanism is for peptides to evolve within a "host" protein and emerge by proteolytic processing. The first examples of such interstitial peptides were ones hosted by precursors for seed storage albumin. Interstitial peptides have also been observed in precursors for seed vicilins, but current evidence for vicilin-buried peptides (VBPs) is limited to seeds of the broadleaf plants pumpkin and macadamia. Here, an extensive sequence analysis of vicilin precursors suggested that peptides buried within the N-terminal region of preprovicilins are widespread and truly ancient. Gene sequences indicative of interstitial peptides were found in species from Amborellales to eudicots and include important grass and legume crop species. We show the first protein evidence for a monocot VBP in date palm seeds as well as protein evidence from other crops including the common tomato, sesame and pumpkin relatives, cucumber, and the sponge loofah ( Luffa aegyptiaca). Their excision was consistent with asparaginyl endopeptidase-mediated maturation, and sequences were confirmed by tandem mass spectrometry. Our findings suggest that the family is large and ancient and that based on the NMR solution structures for loofah Luffin P1 and tomato VBP-8, VBPs adopt a helical hairpin fold stapled by two internal disulfide bonds. The first VBPs characterized were a protease inhibitor, antimicrobials, and a ribosome inactivator. The age and evolutionary retention of this peptide family suggest its members play important roles in plant biology.


    Organizational Affiliation

    Faculty of Medicine, School of Biomedical Sciences , The University of Queensland , Brisbane , Queensland 4072 , Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VicilinA49Solanum lycopersicumMutation(s): 0 
Gene Names: vicilin
UniProt
Find proteins for B0JEU3 (Solanum lycopersicum)
Explore B0JEU3 
Go to UniProtKB:  B0JEU3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with acceptable covalent geometry 
  • OLDERADO: 6O3Q Olderado

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP190102058

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence