4EJF

Allosteric peptides that bind to a caspase zymogen and mediate caspase tetramerization


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6465 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Allosteric peptides bind a caspase zymogen and mediate caspase tetramerization.

Stanger, K.Steffek, M.Zhou, L.Pozniak, C.D.Quan, C.Franke, Y.Tom, J.Tam, C.Elliott, J.M.Lewcock, J.W.Zhang, Y.Murray, J.Hannoush, R.N.

(2012) Nat.Chem.Biol. 8: 655-660

  • DOI: 10.1038/nchembio.967

  • PubMed Abstract: 
  • The caspases are a family of cytosolic proteases with essential roles in inflammation and apoptosis. Drug discovery efforts have focused on developing molecules directed against the active sites of caspases, but this approach has proved challenging a ...

    The caspases are a family of cytosolic proteases with essential roles in inflammation and apoptosis. Drug discovery efforts have focused on developing molecules directed against the active sites of caspases, but this approach has proved challenging and has not yielded any approved therapeutics. Here we describe a new strategy for generating inhibitors of caspase-6, a potential therapeutic target in neurodegenerative disorders, by screening against its zymogen form. Using phage display to discover molecules that bind the zymogen, we report the identification of a peptide that specifically impairs the function of caspase-6 in vitro and in neuronal cells. Remarkably, the peptide binds at a tetramerization interface that is uniquely present in zymogen caspase-6, rather than binding into the active site, and acts via a new allosteric mechanism that promotes caspase tetramerization. Our data illustrate that screening against the zymogen holds promise as an approach for targeting caspases in drug discovery.


    Organizational Affiliation

    Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase-6
A, B, C, D
279Homo sapiensMutation(s): 1 
Gene Names: CASP6 (MCH2)
EC: 3.4.22.59
Find proteins for P55212 (Homo sapiens)
Go to Gene View: CASP6
Go to UniProtKB:  P55212
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
phage-derived peptide 419
E, F, G, H
18N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6465 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 128.299α = 90.00
b = 105.692β = 106.61
c = 91.924γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-04-06 
  • Released Date: 2012-06-20 
  • Deposition Author(s): Murray, J.M.

Revision History 

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-07-18
    Type: Derived calculations
  • Version 1.2: 2012-09-05
    Type: Database references