5NIJ

Crystal structure of arabidopsis thaliana legumain isoform gamma in two-chain activation state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of Plant Legumain Reveals a Unique Two-Chain State with pH-Dependent Activity Regulation.

Zauner, F.B.Dall, E.Regl, C.Grassi, L.Huber, C.G.Cabrele, C.Brandstetter, H.

(2018) Plant Cell 30: 686-699

  • DOI: 10.1105/tpc.17.00963

  • PubMed Abstract: 
  • The vacuolar cysteine protease legumain can cleave and selectively rebuild peptide bonds, thereby vastly expanding the sequential repertoire of biomolecules. In this context, plant legumains have recently at-tracted particular interest. Furthermore, ...

    The vacuolar cysteine protease legumain can cleave and selectively rebuild peptide bonds, thereby vastly expanding the sequential repertoire of biomolecules. In this context, plant legumains have recently at-tracted particular interest. Furthermore, legumains have important roles in many physiological pro-cesses, including programmed cell death. Their efficient peptide bond ligase activity has gained tremen-dous interest in the design of cyclic peptides for drug design. However, the mechanistic understanding of these dual activities is incomplete and partly conflicting. Here we present the crystal structure of a plant legumain, Arabidopsis thaliana isoform-γ (AtLEGγ). Employing a conserved legumain fold, the plant legumain AtLEGγ revealed unique mechanisms of auto-activation, including a plant-specific two-chain activation state, which remains conformationally stable at neutral pH, which is a prerequisite for full ligase activity and survival in different cell compartments. The charge distribution around the α6-helix mediates the pH-dependent dimerization and serves as a gatekeeper for the active site, thus regulating its protease and ligase activity.


    Organizational Affiliation

    University of Salzburg CITY: Salzburg Austria [AT].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vacuolar-processing enzyme gamma-isozyme
A, B, C, D
454Arabidopsis thalianaMutation(s): 0 
EC: 3.4.22.34
Find proteins for Q39119 (Arabidopsis thaliana)
Go to UniProtKB:  Q39119
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SNN
Query on SNN
A, B, C, D
L-PEPTIDE LINKINGC4 H6 N2 O2ASN
SCH
Query on SCH
A, B, C, D
L-PEPTIDE LINKINGC4 H9 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.214 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 147.830α = 90.00
b = 147.830β = 90.00
c = 101.600γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaW_01213

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-04-18
    Type: Data collection, Database references