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 

wwPDB Validation   3D Report Full Report


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 subnanomolar inhibition constant and, in contrast to the peptidic caspase inhibitors, with very high specificity for this particular caspase ...

    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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-2A, D [auth C], G [auth E], J [auth G], M [auth I], P [auth K]169Homo sapiensMutation(s): 1 
Gene Names: CASP2ICH1NEDD2
EC: 3.4.22 (PDB Primary Data), 3.4.22.55 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42575 (Homo sapiens)
Explore P42575 
Go to UniProtKB:  P42575
PHAROS:  P42575
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-2B, E [auth D], H [auth F], K [auth H], N [auth J], Q [auth L]106Homo sapiensMutation(s): 0 
Gene Names: CASP2ICH1NEDD2
EC: 3.4.22 (PDB Primary Data), 3.4.22.55 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42575 (Homo sapiens)
Explore P42575 
Go to UniProtKB:  P42575
PHAROS:  P42575
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-2C [auth P], F [auth Q], I [auth R], L [auth S], O [auth T], R [auth U]169Homo 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  (Full details and data files)

  • 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