6SH2

Crystal structure of human neprilysin E584D in complex with C-type natriuretic peptide.

PDB DOI: https://doi.org/10.2210/pdb6SH2/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Komagataella phaffii GS115
Mutation(s): Yes

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.287
R-Value Work: 0.243

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 80.83 kDa
Atom Count: 5,535
Modelled Residue Count: 700
Deposited Residue Count: 700
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neprilysin	A [auth AAA]	696	Homo sapiens	Mutation(s): 1 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08473
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A [auth AAA]	Go to GlyGen: P08473-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-type natriuretic peptide fragment (CNP)	B [auth DDD]	4	Homo sapiens	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain D [auth AAA] SDF format, chain E [auth AAA] SDF format, chain F [auth AAA] MOL2 format, chain C [auth AAA] MOL2 format, chain D [auth AAA] MOL2 format, chain E [auth AAA] MOL2 format, chain F [auth AAA] mmCIF format, chain C [auth AAA] mmCIF format, chain D [auth AAA] mmCIF format, chain E [auth AAA] mmCIF format, chain F [auth AAA]	C [auth AAA], D [auth AAA], E [auth AAA], F [auth AAA]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth AAA] Focus chain E [auth AAA] Focus chain F [auth AAA]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth AAA] MOL2 format, chain G [auth AAA] mmCIF format, chain G [auth AAA]	G [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth AAA] Interactions & Density Focus chain G [auth AAA]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth AAA] SDF format, chain I [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain I [auth AAA] mmCIF format, chain H [auth AAA] mmCIF format, chain I [auth AAA]	H [auth AAA], I [auth AAA]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth AAA] Focus chain I [auth AAA] Interactions & Density Focus chain H [auth AAA] Focus chain I [auth AAA]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.287
R-Value Work: 0.243
Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.267	α = 90
b = 109.267	β = 90
c = 112.579	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-09-25

Deposition Author(s):

Moss, S.

Subramanian, V.

Acharya, K.R.

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

Revision History (Full details and data files)

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: 2024-10-16
Changes: Structure summary