6AZT

Asparaginyl endopeptidase 1 bound to AAN peptide, a tetrahedral intermediate

  • Classification: PLANT PROTEIN
  • Expression System: Escherichia coli

  • Deposited: 2017-09-13 Released: 2018-02-07 
  • Deposition Author(s): Bond, C.S.
  • Funding Organization(s): Australian Research Council 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis of ribosomal peptide macrocyclization in plants.

Haywood, J.Schmidberger, J.W.James, A.M.Nonis, S.G.Sukhoverkov, K.V.Elias, M.Bond, C.S.Mylne, J.S.

(2018) Elife 7: --

  • DOI: 10.7554/eLife.32955

  • PubMed Abstract: 
  • Constrained, cyclic peptides encoded by plant genes represent a new generation of drug leads. Evolution has repeatedly recruited the Cys-protease asparaginyl endopeptidase (AEP) to perform their head-to-tail ligation. These macrocyclization reactions ...

    Constrained, cyclic peptides encoded by plant genes represent a new generation of drug leads. Evolution has repeatedly recruited the Cys-protease asparaginyl endopeptidase (AEP) to perform their head-to-tail ligation. These macrocyclization reactions use the substrates amino terminus instead of water to deacylate, so a peptide bond is formed. How solvent-exposed plant AEPs macrocyclize is poorly understood. Here we present the crystal structure of an active plant AEP from the common sunflower, Helianthus annuus. The active site contained electron density for a tetrahedral intermediate with partial occupancy that predicted a binding mode for peptide macrocyclization. By substituting catalytic residues we could alter the ratio of cyclic to acyclic products. Moreover, we showed AEPs from other species lacking cyclic peptides can perform macrocyclization under favorable pH conditions. This structural characterization of AEP presents a logical framework for engineering superior enzymes that generate macrocyclic peptide drug leads.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Asparaginyl endopeptidase 1
A
491N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALA-ALA-ASN tetrahedral intermediate
B
3N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
IAS
Query on IAS
A
L-beta-peptide, C-gamma linkingC4 H7 N O4

--

CE7
Query on CE7
B
L-peptide linkingC4 H10 N2 O4ASN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.152 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 77.030α = 90.00
b = 77.030β = 90.00
c = 108.171γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
iMOSFLMdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-09-13 
  • Released Date: 2018-02-07 
  • Deposition Author(s): Bond, C.S.

Funding OrganizationCountryGrant Number
Australian Research CouncilAustraliaDP160100107

Revision History 

  • Version 1.0: 2018-02-07
    Type: Initial release