5A24

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

Summary for 5A24

• Entry DOI: 10.2210/pdb5a24/pdb
• Descriptor: DIONAIN-1, N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: hydrolase, cysteine peptidase, venus flytrap, digestive enzyme, acidic enzyme
• Biological source: DIONAEA MUSCIPULA (VENUS FLYTRAP)
• Total number of polymer chains: 1
• Total formula weight: 23492.31

Authors

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. (deposition date: 2015-05-12, release date: 2015-12-09, Last modification date: 2024-01-10)

Primary citation

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.
Enzymatic and Structural Characterization of the Major Endopeptidase in the Venus Flytrap Digestion Fluid.
J.Biol.Chem., 291:2271-, 2016

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.

PubMed: 26627834
DOI: 10.1074/JBC.M115.672550

Experimental method

X-RAY DIFFRACTION (1.5 Å)