4EJF

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

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
  • Primary Citation of Related Structures:  
    4EJF

  • 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 and has not yielded any approved therapeutics ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-6 A, B, C, D279Homo sapiensMutation(s): 1 
Gene Names: CASP6, MCH2
EC: 3.4.22.59
Find proteins for P55212 (Homo sapiens)
Explore P55212 
Go to UniProtKB:  P55212
NIH Common Fund Data Resources
PHAROS:  P55212
GTEx:  ENSG00000138794
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
phage-derived peptide 419 E, F, G, H18synthetic constructMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4
Download Ideal Coordinates CCD File 
C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.299α = 90
b = 105.692β = 106.61
c = 91.924γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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