4Y6K

Complex structure of presenilin homologue PSH bound to an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.855 Å
  • R-Value Free: 0.367 
  • R-Value Work: 0.320 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cleavage of amyloid precursor protein by an archaeal presenilin homologue PSH

Dang, S.Wu, S.Wang, J.Li, H.Huang, M.He, W.Li, Y.M.Wong, C.C.Shi, Y.

(2015) Proc.Natl.Acad.Sci.USA 112: 3344-3349

  • DOI: 10.1073/pnas.1502150112

  • PubMed Abstract: 
  • Aberrant cleavage of amyloid precursor protein (APP) by γ-secretase contributes to the development of Alzheimer's disease. More than 200 disease-derived mutations have been identified in presenilin (the catalytic subunit of γ-secretase), making modul ...

    Aberrant cleavage of amyloid precursor protein (APP) by γ-secretase contributes to the development of Alzheimer's disease. More than 200 disease-derived mutations have been identified in presenilin (the catalytic subunit of γ-secretase), making modulation of γ-secretase activity a potentially attractive therapeutic opportunity. Unfortunately, the technical challenges in dealing with intact γ-secretase have hindered discovery of modulators and demand a convenient substitute approach. Here we report that, similar to γ-secretase, the archaeal presenilin homolog PSH faithfully processes the substrate APP C99 into Aβ42, Aβ40, and Aβ38. The molar ratio of the cleavage products Aβ42 over Aβ40 by PSH is nearly identical to that by γ-secretase. The proteolytic activity of PSH is specifically suppressed by presenilin-specific inhibitors. Known modulators of γ-secretase also modulate PSH similarly in terms of the Aβ42/Aβ40 ratio. Structural analysis reveals association of a known γ-secretase inhibitor with PSH between its two catalytic aspartate residues. These findings identify PSH as a surrogate protease for the screening of agents that may regulate the protease activity and the cleavage preference of γ-secretase.


    Organizational Affiliation

    Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein PSH
A, B, C, D
301Methanoculleus marisnigri (strain ATCC 35101 / DSM 1498 / JR1)Mutation(s): 5 
Find proteins for A3CWV0 (Methanoculleus marisnigri (strain ATCC 35101 / DSM 1498 / JR1))
Go to UniProtKB:  A3CWV0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4B5
Query on 4B5

Download SDF File 
Download CCD File 
C, D
N-{(2R,4S,5S)-2-benzyl-5-[(tert-butoxycarbonyl)amino]-4-hydroxy-6-phenylhexanoyl}-L-leucyl-L-phenylalaninamide
C39 H52 N4 O6
MURCDOXDAHPNRQ-OWIQAHIBSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002147 (4B5)
Query on PRD_002147
C,DN-{(2R,4S,5S)-2-benzyl-5-[(tert-butoxycarbonyl)amino]-4-hydroxy-6-phenylhexanoyl}-L-leucyl-L-phenylalaninamidePeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.855 Å
  • R-Value Free: 0.367 
  • R-Value Work: 0.320 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 168.617α = 90.00
b = 201.691β = 90.00
c = 117.505γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-03-25
    Type: Non-polymer description
  • Version 1.2: 2015-04-08
    Type: Database references