4CTH

Neprilysin variant G399V,G714K in complex with phosphoramidon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Engineering Neprilysin Activity and Specificity to Create a Novel Therapeutic for Alzheimer'S Disease.

Webster, C.I.Burrell, M.Olsson, L.Fowler, S.B.Digby, S.Sandercock, A.Snijder, A.Tebbe, J.Haupts, U.Grudzinska, J.Jermutus, L.Andersson, C.

(2014) Plos One 9: 04001

  • DOI: 10.1371/journal.pone.0104001

  • PubMed Abstract: 
  • Neprilysin is a transmembrane zinc metallopeptidase that degrades a wide range of peptide substrates. It has received attention as a potential therapy for Alzheimer's disease due to its ability to degrade the peptide amyloid beta. However, its broad ...

    Neprilysin is a transmembrane zinc metallopeptidase that degrades a wide range of peptide substrates. It has received attention as a potential therapy for Alzheimer's disease due to its ability to degrade the peptide amyloid beta. However, its broad range of peptide substrates has the potential to limit its therapeutic use due to degradation of additional peptides substrates that tightly regulate many physiological processes. We sought to generate a soluble version of the ectodomain of neprilysin with improved activity and specificity towards amyloid beta as a potential therapeutic for Alzheimer's disease. Extensive amino acid substitutions were performed at positions surrounding the active site and inner surface of the enzyme and variants screened for activity on amyloid beta 1-40, 1-42 and a variety of other physiologically relevant peptides. We identified several mutations that modulated and improved both enzyme selectivity and intrinsic activity. Neprilysin variant G399V/G714K displayed an approximately 20-fold improved activity on amyloid beta 1-40 and up to a 3,200-fold reduction in activity on other peptides. Along with the altered peptide substrate specificity, the mutant enzyme produced a markedly altered series of amyloid beta cleavage products compared to the wild-type enzyme. Crystallisation of the mutant enzyme revealed that the amino acid substitutions result in alteration of the shape and size of the pocket containing the active site compared to the wild-type enzyme. The mutant enzyme offers the potential for the more efficient degradation of amyloid beta in vivo as a therapeutic for the treatment of Alzheimer's disease.


    Organizational Affiliation

    Antibody Discovery and Protein Engineering, MedImmune, Cambridge, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NEPRILYSIN
A
709Homo sapiensMutation(s): 2 
Gene Names: MME (EPN)
EC: 3.4.24.11
Find proteins for P08473 (Homo sapiens)
Go to Gene View: MME
Go to UniProtKB:  P08473
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
RDF
Query on RDF

Download SDF File 
Download CCD File 
A
N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN
PHOSPHORAMIDON
C23 H34 N3 O10 P
ZPHBZEQOLSRPAK-XLCYBJAPSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000638 (RDF)
Query on PRD_000638
APHOSPHORAMIDONGlycopeptide / Enzyme inhibitor

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RDFKi: 4 nM (93) BINDINGDB
RDFIC50: 0.4 - 200 nM (93) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.209 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 108.799α = 90.00
b = 108.799β = 90.00
c = 112.942γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
MOSFLMdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2018-06-20
    Type: Data collection, Structure summary