2EWY

Crystal structure of human BACE2 in complex with a hydroxyethylenamine transition-state inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of human BACE2 in complex with a hydroxyethylamine transition state inhibitor

Ostermann, N.Eder, J.Eidhoff, U.Zink, F.Hassiepen, U.Worpenberg, S.Maibaum, J.Simic, O.Hommel, U.Gerhartz, B.

(2006) J.Mol.Biol. 355: 249-261

  • DOI: 10.1016/j.jmb.2005.10.027

  • PubMed Abstract: 
  • BACE2 is a membrane-bound aspartic protease of the A1 family with a high level of sequence homology to BACE1. While BACE1 is involved in the generation of amyloid plaques in Alzheimer's disease by cleaving Abeta-peptides from the amyloid precursor pr ...

    BACE2 is a membrane-bound aspartic protease of the A1 family with a high level of sequence homology to BACE1. While BACE1 is involved in the generation of amyloid plaques in Alzheimer's disease by cleaving Abeta-peptides from the amyloid precursor protein, the physiological function of BACE2 is not well understood. BACE2 appears to be associated with the early onset of dementia in patients with Down's syndrome, and it has been shown to be highly expressed in breast cancers. Further, it may participate in the function of normal and abnormal processes of human muscle biology. Similar to other aspartic proteases, BACE2 is expressed as an inactive zymogen requiring the cleavage of its pro-sequence during the maturation process. We have produced mature BACE2 by expression of pro-BACE2 in Escherichia coli as inclusion bodies, followed by refolding and autocatalytic activation at pH 3.4. Using a C and N-terminally truncated BACE2 variant, we were able to crystallize and determine the crystal structure of mature BACE2 in complex with a hydroxyethylamine transition-state mimetic inhibitor at 3.1 angstroms resolution. The structure of BACE2 follows the general fold of A1 aspartic proteases. However, similar to BACE1, its C-terminal domain is significantly larger than that of the other family members. Furthermore, the structure of BACE2 reveals differences in the S3, S2, S1' and S2' active site substrate pockets as compared to BACE1, and allows, therefore, for a deeper understanding of the structural features that may facilitate the design of selective BACE1 or BACE2 inhibitors.


    Organizational Affiliation

    Protease Platform, Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland. nils.ostermann@novartis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-secretase 2
A, B, C, D
383Homo sapiensMutation(s): 0 
Gene Names: BACE2 (AEPLC, ALP56, ASP21)
EC: 3.4.23.45
Find proteins for Q9Y5Z0 (Homo sapiens)
Go to Gene View: BACE2
Go to UniProtKB:  Q9Y5Z0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DBO
Query on DBO

Download SDF File 
Download CCD File 
A, B, C, D
N-{(1S,2R)-1-BENZYL-2-HYDROXY-3-[(3-METHYLBENZYL)AMINO]PROPYL}DIBENZO[B,F]OXEPINE-10-CARBOXAMIDE
C33 H32 N2 O3
BNWZCXDHHPBQOX-XZWHSSHBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DBOIC50: 700 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.227 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 228.407α = 90.00
b = 228.407β = 90.00
c = 108.964γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNXrefinement
DENZOdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-11-07 
  • Released Date: 2006-11-07 
  • Deposition Author(s): Ostermann, N.

Revision History 

  • Version 1.0: 2006-11-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance