6SH1

Crystal structure of substrate-free human neprilysin E584D.

• PDB DOI: https://doi.org/10.2210/pdb6SH1/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Komagataella phaffii GS115
• Mutation(s): No 


• Deposited: 2019-08-05 Released: 2019-09-25 
• Deposition Author(s): Moss, S., Subramanian, V., Acharya, K.R.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.261 
• R-Value Work: 0.218 

Starting Model: experimental

Literature

Crystal structure of peptide-bound neprilysin reveals key binding interactions.

Moss, S., Subramanian, V., Acharya, K.R.

(2020) FEBS Lett 594: 327-336

• PubMed: 31514225 
• DOI: https://doi.org/10.1002/1873-3468.13602
• Primary Citation of Related Structures:  
  6SH1, 6SH2


• PubMed Abstract: 
  

  Neprilysin (NEP) is a promiscuous zinc metalloprotease with broad substrate specificity and cleaves a remarkable diversity of substrates through endopeptidase action. Two of these - amyloid-β and natriuretic peptides - implicate the enzyme in both Alzheimer's disease and cardiovascular disease, respectively. Here, we report the creation of a catalytically inactive NEP (E584D) to determine the first peptide-bound crystal structure at 2.6 Å resolution. The structure reveals key interactions involved in substrate binding which we have identified to be conserved in other known zinc metalloproteases. In addition, the structure provides evidence for a potential exosite within the central cavity that may play a critical role in substrate positioning. Together, these results contribute to our understanding of the molecular function of NEP.

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Organizational Affiliation: 

Department of Biology and Biochemistry, Claverton Down, University of Bath, UK.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 161.11 kDa 
• Atom Count: 11,723 
• Modelled Residue Count: 1,392 
• Deposited Residue Count: 1,392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neprilysin	A [auth AAA], B [auth CCC]	696	Homo sapiens	Mutation(s): 0  Gene Names: MME, EPN 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
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: P08473-1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth AAA], D [auth AAA], E [auth AAA], F [auth AAA], I [auth CCC], J [auth CCC], K [auth CCC], L [auth CCC]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	H [auth AAA], O [auth CCC]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	G [auth AAA], M [auth CCC], N [auth CCC]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.261 
• R-Value Work: 0.218 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.14	α = 90
b = 99.745	β = 106.231
c = 100.119	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-25 
Deposition Author(s): Moss, S., Subramanian, V., Acharya, K.R.

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Funding Organization	Location	Grant Number
Other private	United Kingdom	286 (AS-PhD2015b006)

Revision History  

• Version 1.0: 2019-09-25
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-11-13
  Changes: Structure summary