6XT5

Jack bean asparaginyl endopeptidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.196 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural and biochemical analyses of concanavalin A circular permutation by jack bean asparaginyl endopeptidase.

Nonis, S.G.Haywood, J.Schmidberger, J.W.Mackie, E.R.R.Soares da Costa, T.P.Bond, C.S.Mylne, J.S.

(2021) Plant Cell 33: 2794-2811

  • DOI: https://doi.org/10.1093/plcell/koab130
  • Primary Citation of Related Structures:  
    6XT5, 6XT6

  • PubMed Abstract: 

    Over 30 years ago, an intriguing posttranslational modification was found responsible for creating concanavalin A (conA), a carbohydrate-binding protein from jack bean (Canavalia ensiformis) seeds and a common carbohydrate chromatography reagent. ConA biosynthesis involves what was then an unprecedented rearrangement in amino-acid sequence, whereby the N-terminal half of the gene-encoded conA precursor (pro-conA) is swapped to become the C-terminal half of conA. Asparaginyl endopeptidase (AEP) was shown to be involved, but its mechanism was not fully elucidated. To understand the structural basis and consequences of circular permutation, we generated recombinant jack bean pro-conA plus jack bean AEP (CeAEP1) and solved crystal structures for each to 2.1 and 2.7 Å, respectively. By reconstituting conA biosynthesis in vitro, we prove CeAEP1 alone can perform both cleavage and cleavage-coupled transpeptidation to form conA. CeAEP1 structural analysis reveals how it is capable of carrying out both reactions. Biophysical assays illustrated that pro-conA is less stable than conA. This observation was explained by fewer intermolecular interactions between subunits in the pro-conA crystal structure and consistent with a difference in the prevalence for tetramerization in solution. These findings elucidate the consequences of circular permutation in the only posttranslation example known to occur in nature.


  • Organizational Affiliation

    School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Legumain
A, B
451Canavalia ensiformisMutation(s): 0 
EC: 3.4.22.34
UniProt
Find proteins for P49046 (Canavalia ensiformis)
Explore P49046 
Go to UniProtKB:  P49046
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49046
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SNN
Query on SNN
A, B
L-PEPTIDE LINKINGC4 H6 N2 O2ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.196 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.989α = 90
b = 88.882β = 111.722
c = 109.848γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
Cootmodel building
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP160100107
Australian Research Council (ARC)AustraliaDE180101445

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-11
    Type: Initial release
  • Version 1.1: 2021-08-25
    Changes: Database references
  • Version 1.2: 2021-09-29
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations