4CTH | pdb_00004cth

Neprilysin variant G399V,G714K in complex with phosphoramidon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.261 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1371/journal.pone.0104001
  • Primary Citation Related Structures: 
    4CTH

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 83.42 kDa 
  • Atom Count: 6,064 
  • Modeled Residue Count: 697 
  • Deposited Residue Count: 709 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NEPRILYSIN709Homo sapiensMutation(s): 2 
EC: 3.4.24.11
UniProt & NIH Common Fund Data Resources
Find proteins for P08473 (Homo sapiens)
Explore P08473 
Go to UniProtKB:  P08473
PHAROS:  P08473
GTEx:  ENSG00000196549 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08473
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P08473-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RDF

Query on RDF



Download:Ideal Coordinates CCD File
N [auth A]N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN
C23 H34 N3 O10 P
ZPHBZEQOLSRPAK-XLCYBJAPSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique
Entity ID: 5
IDChains NameType/Class2D Diagram3D Interactions
PRD_000638 (RDF)
Query on PRD_000638
N [auth A]PHOSPHORAMIDONGlycopeptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.261 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.799α = 90
b = 108.799β = 90
c = 112.942γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Structure summary
  • Version 1.2: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.5: 2024-11-13
    Changes: Structure summary