6AZT | pdb_00006azt

Asparaginyl endopeptidase 1 bound to AAN peptide, a tetrahedral intermediate

• PDB DOI: https://doi.org/10.2210/pdb6AZT/pdb

• Classification: PLANT PROTEIN
• Organism(s): Helianthus annuus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

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

• PubMed: 29384475 
• DOI: https://doi.org/10.7554/eLife.32955
• Primary Citation Related Structures: 
  6AZT


• 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 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.

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Organizational Affiliation: 
• School of Molecular Sciences, The University of Western Australia, Perth, Australia.
The ARC Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, Australia.
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 54.89 kDa 
• Atom Count: 2,415 
• Modeled Residue Count: 277 
• Deposited Residue Count: 494 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Asparaginyl endopeptidase 1	A	491	Helianthus annuus	Mutation(s): 0  Gene Names: AEP1 EC: 3.4.22.34
UniProt
Find proteins for A0A251RPF5 (Helianthus annuus) Explore A0A251RPF5  Go to UniProtKB:  A0A251RPF5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-ALA-ASN tetrahedral intermediate	B	3	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNN	A	L-PEPTIDE LINKING	C4 H6 N2 O2		ASN
CE7	B	L-PEPTIDE LINKING	C4 H10 N2 O4		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.03	α = 90
b = 77.03	β = 90
c = 108.171	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	DP160100107

Revision History  

• Version 1.0: 2018-02-07
  Type: Initial release
  
• Version 2.0: 2018-05-16
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
• Version 2.1: 2020-01-01
  Changes: Author supporting evidence
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations