2P2C

Inhibition of caspase-2 by a designed ankyrin repeat protein (DARPin)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.262 

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This is version 1.3 of the entry. See complete history. 


Literature

Inhibition of Caspase-2 by a Designed Ankyrin Repeat Protein: Specificity, Structure, and Inhibition Mechanism.

Schweizer, A., Roschitzki-Voser, H., Amstutz, P., Briand, C., Gulotti-Georgieva, M., Prenosil, E., Binz, H.K., Capitani, G., Baici, A., Pluckthun, A., Grutter, M.G.

(2007) Structure 15: 625-636

  • DOI: 10.1016/j.str.2007.03.014
  • Primary Citation of Related Structures:  
    2P2C

  • PubMed Abstract: 

    • Specific and potent caspase inhibitors are indispensable for the dissection of the intricate pathways leading to apoptosis. We selected a designed ankyrin repeat protein (DARPin) from a combinatorial library that inhibits caspase-2 in vitro with a subnan ...

    Specific and potent caspase inhibitors are indispensable for the dissection of the intricate pathways leading to apoptosis. We selected a designed ankyrin repeat protein (DARPin) from a combinatorial library that inhibits caspase-2 in vitro with a subnanomolar inhibition constant and, in contrast to the peptidic caspase inhibitors, with very high specificity for this particular caspase. The crystal structure of this inhibitor (AR_F8) in complex with caspase-2 reveals the molecular basis for the specificity and, together with kinetic analyses, the allosteric mechanism of inhibition. The structure also shows a conformation of the active site that can be exploited for the design of inhibitory compounds. AR_F8 is a specific inhibitor of an initiator caspase and has the potential to help identify the function of caspase-2 in the complex biological apoptotic signaling network.

    Organizational Affiliation: 

    Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-2 A, C, E, G, I, K169Homo sapiensMutation(s): 1 
Gene Names: CASP2, ICH1, NEDD2
EC: 3.4.22 (PDB Primary Data), 3.4.22.55 (UniProt)
Find proteins for P42575 (Homo sapiens)
Explore P42575 
Go to UniProtKB:  P42575
NIH Common Fund Data Resources
PHAROS:  P42575
GTEx:  ENSG00000106144
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-2 B, D, F, H, J, L106Homo sapiensMutation(s): 0 
Gene Names: CASP2, ICH1, NEDD2
EC: 3.4.22 (PDB Primary Data), 3.4.22.55 (UniProt)
Find proteins for P42575 (Homo sapiens)
Explore P42575 
Go to UniProtKB:  P42575
NIH Common Fund Data Resources
PHAROS:  P42575
GTEx:  ENSG00000106144
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-2 P, Q, R, S, T, U169Homo sapiensMutation(s): 0 
Gene Names: CASP2
EC: 3.4.22
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.24 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.262 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.02α = 90
b = 229.21β = 90.11
c = 114.93γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Structure summary