Crystal Structure of the mature form of the glutamic-class prolyl-endopeptidase neprosin at 2.35 A resolution.

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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Molecular and in vivo studies of a glutamate-class prolyl-endopeptidase for coeliac disease therapy.

Del Amo-Maestro, L.Mendes, S.R.Rodriguez-Banqueri, A.Garzon-Flores, L.Girbal, M.Rodriguez-Lagunas, M.J.Guevara, T.Franch, A.Perez-Cano, F.J.Eckhard, U.Gomis-Ruth, F.X.

(2022) Nat Commun 13: 4446-4446

  • DOI: https://doi.org/10.1038/s41467-022-32215-1
  • Primary Citation of Related Structures:  
    7ZU8, 7ZVA, 7ZVB, 7ZVC

  • PubMed Abstract: 

    The digestion of gluten generates toxic peptides, among which a highly immunogenic proline-rich 33-mer from wheat α-gliadin, that trigger coeliac disease. Neprosin from the pitcher plant is a reported prolyl endopeptidase. Here, we produce recombinant neprosin and its mutants, and find that full-length neprosin is a zymogen, which is self-activated at gastric pH by the release of an all-β pro-domain via a pH-switch mechanism featuring a lysine plug. The catalytic domain is an atypical 7+8-stranded β-sandwich with an extended active-site cleft containing an unprecedented pair of catalytic glutamates. Neprosin efficiently degrades both gliadin and the 33-mer in vitro under gastric conditions and is reversibly inactivated at pH > 5. Moreover, co-administration of gliadin and the neprosin zymogen at the ratio 500:1 reduces the abundance of the 33-mer in the small intestine of mice by up to 90%. Neprosin therefore founds a family of eukaryotic glutamate endopeptidases that fulfils requisites for a therapeutic glutenase.

  • Organizational Affiliation

    Proteolysis Laboratory; Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park; c/Baldiri Reixac, 15-21, 08028, Barcelona, Catalonia, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-terminal peptidase261Nepenthes ventricosa x Nepenthes alataMutation(s): 0 
Find proteins for A0A1L7NZU4 (Nepenthes alata)
Explore A0A1L7NZU4 
Go to UniProtKB:  A0A1L7NZU4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L7NZU4
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G09724ZC
GlyCosmos:  G09724ZC
GlyGen:  G09724ZC
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.76α = 90
b = 49.95β = 106.57
c = 59.86γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-10
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description