6DHI

Butelase 1: Auto-Catalytic Cleavage as an Evolutionary Constraint for Macrocyclizing Endopeptidases

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.276 

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This is version 1.3 of the entry. See complete history. 


Literature

The macrocyclizing protease butelase 1 remains autocatalytic and reveals the structural basis for ligase activity.

James, A.M., Haywood, J., Leroux, J., Ignasiak, K., Elliott, A.G., Schmidberger, J.W., Fisher, M.F., Nonis, S.G., Fenske, R., Bond, C.S., Mylne, J.S.

(2019) Plant J 98: 988-999

  • DOI: 10.1111/tpj.14293
  • Primary Citation of Related Structures:  
    6DHI

  • PubMed Abstract: 

    • Plant asparaginyl endopeptidases (AEPs) are expressed as inactive zymogens that perform maturation of seed storage protein upon cleavage-dependent autoactivation in the low-pH environment of storage vacuoles. The AEPs have attracted attention for their macrocyclization reactions, and have been classified as cleavage or ligation specialists ...

    Plant asparaginyl endopeptidases (AEPs) are expressed as inactive zymogens that perform maturation of seed storage protein upon cleavage-dependent autoactivation in the low-pH environment of storage vacuoles. The AEPs have attracted attention for their macrocyclization reactions, and have been classified as cleavage or ligation specialists. However, we have recently shown that the ability of AEPs to produce either cyclic or acyclic products can be altered by mutations to the active site region, and that several AEPs are capable of macrocyclization given favorable pH conditions. One AEP extracted from Clitoria ternatea seeds (butelase 1) is classified as a ligase rather than a protease, presenting an opportunity to test for loss of cleavage activity. Here, making recombinant butelase 1 and rescuing an Arabidopsis thaliana mutant lacking AEP, we show that butelase 1 retains cleavage functions in vitro and in vivo. The in vivo rescue was incomplete, consistent with some trade-off for butelase 1 specialization toward macrocyclization. Its crystal structure showed an active site with only subtle differences from cleaving AEPs, suggesting the many differences in its peptide-binding region are the source of its efficient macrocyclization. All considered, it seems that either butelase 1 has not fully specialized or a requirement for autocatalytic cleavage is an evolutionary constraint upon macrocyclizing AEPs.

    Organizational Affiliation: 

    The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, 6009, Australia.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Asparaginyl endopeptidaseA, B, C, D473Clitoria ternateaMutation(s): 0 
EC: 3.4.22.34
UniProt
Find proteins for A0A060D9Z7 (Clitoria ternatea)
Explore A0A060D9Z7 
Go to UniProtKB:  A0A060D9Z7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A060D9Z7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SNN
Query on SNN		A, B, C, D L-PEPTIDE LINKINGC4 H6 N2 O2ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.274 
  • R-Value Observed: 0.276 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.36α = 90
b = 147.687β = 90
c = 183.334γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP160100107

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence