7ZU8 | pdb_00007zu8

Crystal Structure of the zymogen form of the glutamic-class prolyl-endopeptidase neprosin at 2.05 A resolution in presence of the crystallophore Lu-Xo4.

• PDB DOI: https://doi.org/10.2210/pdb7ZU8/pdb

• Classification: HYDROLASE
• Organism(s): Nepenthes ventricosa x Nepenthes alata
• Expression System: Homo sapiens neanderthalensis
• Mutation(s): No 


• Deposited: 2022-05-11 Released: 2022-08-10 
• Deposition Author(s): Del Amo-Maestro, L., Eckhard, U., Rodriguez-Banqueri, A., Mendes, S.R., Guevara, T., Gomis-Ruth, F.X.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.250 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

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

• PubMed: 35915115 
• 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.

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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.
Section of Physiology; Department of Biochemistry and Physiology; Faculty of Pharmacy and Food Science, University of Barcelona, Av. Joan XXIII, 27-31, 08028, Barcelona, Catalonia, Spain.
Research Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, Av. Prat de la Riba, 171, 08921, Santa Coloma de Gramenet, Catalonia, Spain.
Proteolysis Laboratory; Department of Structural Biology, Molecular Biology Institute of Barcelona (CSIC), Barcelona Science Park; c/Baldiri Reixac, 15-21, 08028, Barcelona, Catalonia, Spain. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.27 kDa 
• Atom Count: 2,929 
• Modeled Residue Count: 336 
• Deposited Residue Count: 389 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamyl endopeptidase Neprosin	A	389	Nepenthes ventricosa x Nepenthes alata	Mutation(s): 0  Gene Names: NvNpr EC: 3.4.21.19
UniProt
Find proteins for A0A1L7NZU4 (Nepenthes alata) Explore A0A1L7NZU4  Go to UniProtKB:  A0A1L7NZU4
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K93	D [auth A], F [auth A]	12-oxidanyl-9,11$l^{3}-dioxa-1$l^{4},19$l^{4},22,27$l^{4},28$l^{4}-pentaza-10$l^{6}-lutetaoctacyclo[17.5.2.1^{3,7}.1^{10,13}.0^{1,10}.0^{10,19}.0^{10,28}.0^{17,27}]octacosa-3,5,7(28),11,13,15,17(27)-heptaen-8-one C20 H24 Lu N5 O4 ZJNYWMGNALTZQP-UHFFFAOYSA-M
ACT	E [auth A], G [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.250 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.65	α = 90
b = 93.35	β = 90
c = 48.69	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
AutoSol	phasing
BUSTER	refinement
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Del Amo-Maestro, L., Eckhard, U., Rodriguez-Banqueri, A., Mendes, S.R., Guevara, T., Gomis-Ruth, F.X.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Structure summary