7ZVA | pdb_00007zva

Crystal Structure of the native zymogen form of the glutamic-class prolyl-endopeptidase neprosin at 1.80 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.218 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7ZVA

This is version 1.2 of the entry. See complete history

Literature

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 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.

Macromolecule Content 

  • Total Structure Weight: 44.79 kDa 
  • Atom Count: 3,015 
  • Modeled Residue Count: 335 
  • Deposited Residue Count: 389 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
C-terminal peptidase389Nepenthes ventricosa x Nepenthes alataMutation(s): 0 
UniProt
Find proteins for A0A1L7NZU4 (Nepenthes alata)
Explore A0A1L7NZU4 
Go to UniProtKB:  A0A1L7NZU4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1L7NZU4
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G86851RC
GlyCosmos: G86851RC
GlyGen: G86851RC
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
IPA

Query on IPA



Download:Ideal Coordinates CCD File
Q [auth A]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.218 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.37α = 90
b = 92.62β = 90
c = 42.69γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTERrefinement
Cootmodel building

Structure Validation

View Full Validation Report



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
  • Version 1.2: 2024-10-16
    Changes: Structure summary