5OBT image
Deposition Date 2017-06-29
Release Date 2018-04-11
Last Version Date 2024-11-06
Entry Detail
PDB ID:
5OBT
Keywords:
Title:
Fully activated A. thaliana legumain isoform gamma in complex with Ac-YVAD-CMK
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.50 Å
R-Value Free:
0.18
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Vacuolar-processing enzyme gamma-isozyme
Gene (Uniprot):F26P21.60
Chain IDs:A, D (auth: B)
Chain Length:245
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Molecule:Ac-YVAD-CMK
Chain IDs:C, F (auth: D)
Chain Length:6
Number of Molecules:2
Biological Source:synthetic construct
Polymer Type:polypeptide(L)
Molecule:Vacuolar-processing enzyme gamma-isozyme
Gene (Uniprot):F26P21.60
Chain IDs:B (auth: E), E (auth: F)
Chain Length:51
Number of Molecules:2
Biological Source:Arabidopsis thaliana
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SNN A ASP modified residue
Peptide-like Molecules
PRD_002086
Primary Citation
Structural analyses ofArabidopsis thalianalegumain gamma reveal differential recognition and processing of proteolysis and ligation substrates.
J. Biol. Chem. 293 8934 8946 (2018)
PMID: 29628443 DOI: 10.1074/jbc.M117.817031

Abstact

Legumain is a dual-function protease-peptide ligase whose activities are of great interest to researchers studying plant physiology and to biotechnological applications. However, the molecular mechanisms determining the specificities for proteolysis and ligation are unclear because structural information on the substrate recognition by a fully activated plant legumain is unavailable. Here, we present the X-ray structure of Arabidopsis thaliana legumain isoform γ (AtLEGγ) in complex with the covalent peptidic Ac-YVAD chloromethyl ketone (CMK) inhibitor targeting the catalytic cysteine. Mapping of the specificity pockets preceding the substrate-cleavage site explained the known substrate preference. The comparison of inhibited and free AtLEGγ structures disclosed a substrate-induced disorder-order transition with synergistic rearrangements in the substrate-recognition sites. Docking and in vitro studies with an AtLEGγ ligase substrate, sunflower trypsin inhibitor (SFTI), revealed a canonical, protease substrate-like binding to the active site-binding pockets preceding and following the cleavage site. We found the interaction of the second residue after the scissile bond, P2'-S2', to be critical for deciding on proteolysis versus cyclization. cis-trans-Isomerization of the cyclic peptide product triggered its release from the AtLEGγ active site and prevented inadvertent cleavage. The presented integrative mechanisms of proteolysis and ligation (transpeptidation) explain the interdependence of legumain and its preferred substrates and provide a rational framework for engineering optimized proteases, ligases, and substrates.

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Primary Citation of related structures