Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 23.49 kDa 
• Atom Count: 1953 
• Residue Count: 222 
• Unique protein chains: 1

5A24

Crystal structure of Dionain-1, the major endopeptidase in the Venus flytrap digestive juice

• DOI: 10.2210/pdb5A24/pdb

• Classification: HYDROLASE
• Organism(s): Dionaea muscipula
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2015-05-12 Released: 2015-12-09 
• Deposition Author(s): Risor, M.W., Thomsen, L.R., Sanggaard, K.W., Nielsen, T.A., Thogersen, I.B., Lukassen, M.V., Rossen, L., Garcia-Ferrer, I., Guevara, T., Meinjohanns, E., Nielsen, N.C., Gomis-Ruth, F.X., Enghild, J.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.172 
• R-Value Work: 0.158 
• R-Value Observed: 0.158 

Literature

Enzymatic and Structural Characterization of the Major Endopeptidase in the Venus Flytrap Digestion Fluid.

Risor, M.W., Thomsen, L.R., Sanggaard, K.W., Nielsen, T.A., Thogersen, I.B., Lukassen, M.V., Rossen, L., Garcia-Ferrer, I., Guevara, T., Scavenius, C., Meinjohanns, E., Gomis-Ruth, F.X., Enghild, J.J.

(2016) J Biol Chem 291: 2271

• PubMed: 26627834 
• DOI: 10.1074/jbc.M115.672550
• Primary Citation of Related Structures:  
  5A24


• PubMed Abstract: 
  

Carnivorous plants primarily use aspartic proteases during digestion of captured prey. In contrast, the major endopeptidases in the digestive fluid of the Venus flytrap (Dionaea muscipula) are cysteine proteases (dionain-1 to -4). Here, we present the crystal structure of mature dionain-1 in covalent complex with inhibitor E-64 at 1.5 Å resolution. The enzyme exhibits an overall protein fold reminiscent of other plant cysteine proteases. The inactive glycosylated pro-form undergoes autoprocessing and self-activation, optimally at the physiologically relevant pH value of 3.6, at which the protective effect of the pro-domain is lost. The mature enzyme was able to efficiently degrade a Drosophila fly protein extract at pH 4 showing high activity against the abundant Lys- and Arg-rich protein, myosin. The substrate specificity of dionain-1 was largely similar to that of papain with a preference for hydrophobic and aliphatic residues in subsite S2 and for positively charged residues in S1. A tentative structure of the pro-domain was obtained by homology modeling and suggested that a pro-peptide Lys residue intrudes into the S2 pocket, which is more spacious than in papain. This study provides the first analysis of a cysteine protease from the digestive fluid of a carnivorous plant and confirms the close relationship between carnivorous action and plant defense mechanisms.

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Organizational Affiliation: 

From the Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark, the Interdisciplinary Nanoscience Center (iNANO), DK-8000 Aarhus, Denmark, [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIONAIN-1	A	222	Dionaea muscipula	Mutation(s): 0
Find proteins for A0A0E3GLN3 (Dionaea muscipula) Explore A0A0E3GLN3  Go to UniProtKB:  A0A0E3GLN3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E64	A	N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE C15 H30 N5 O5 QPQNJAXBPHVASB-QWRGUYRKSA-O
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.172 
• R-Value Work: 0.158 
• R-Value Observed: 0.158 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.85	α = 90
b = 47.79	β = 92.44
c = 57.79	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-05-12 
• Released Date: 2015-12-09 
Deposition Author(s): Risor, M.W., Thomsen, L.R., Sanggaard, K.W., Nielsen, T.A., Thogersen, I.B., Lukassen, M.V., Rossen, L., Garcia-Ferrer, I., Guevara, T., Meinjohanns, E., Nielsen, N.C., Gomis-Ruth, F.X., Enghild, J.J.

Revision History 

• Version 1.0: 2015-12-09
  Type: Initial release
  
• Version 1.1: 2015-12-16
  Changes: Database references
• Version 1.2: 2016-02-10
  Changes: Database references