1PYO

Crystal Structure of Human Caspase-2 in Complex with Acetyl-Leu-Asp-Glu-Ser-Asp-cho


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of caspase-2, apical initiator of the intrinsic apoptotic pathway.

Schweizer, A.Briand, C.Grutter, M.G.

(2003) J Biol Chem 278: 42441-42447

  • DOI: 10.1074/jbc.M304895200
  • Primary Citation of Related Structures:  
    1PYO

  • PubMed Abstract: 
  • The cell death protease caspase-2 has recently been recognized as the most apical caspase in the apoptotic cascade ignited during cell stress signaling. Cytotoxic stress, such as that caused by cancer therapies, leads to activation of caspase-2, whic ...

    The cell death protease caspase-2 has recently been recognized as the most apical caspase in the apoptotic cascade ignited during cell stress signaling. Cytotoxic stress, such as that caused by cancer therapies, leads to activation of caspase-2, which acts as a direct effector of the mitochondrion-dependent apoptotic pathway resulting in programmed cell death. Here we report the x-ray structure of caspase-2 in complex with the inhibitor acetyl-Leu-Asp-Glu-Ser-Asp-aldehyde at 1.65-A resolution. Compared with other caspases, significant structural differences prevail in the active site region and the dimer interface. The structure reveals the hydrophobic properties of the S5 specificity pocket, which is unique to caspase-2, and provides the details of the inhibitor-protein interactions in subsites S1-S4. These features form the basis of caspase-2 specificity and allow the design of caspase-2-directed ligands for medical and analytical use. Another unique feature of caspase-2 is a disulfide bridge at the dimer interface, which covalently links the two monomers. Consistent with this finding, caspase-2 exists as a (p19/p12)2 dimer in solution, even in the absence of substrates or inhibitors. The intersubunit disulfide bridge stabilizes the dimeric form of caspase-2, whereas all other long prodomain caspases exist as monomers in solution, and dimer formation is driven by ligand binding. Therefore, the central disulfide bridge appears to represent a novel way of dimer stabilization in caspases.


    Organizational Affiliation

    Department of Biochemistry, University of Zurich, 8057-Zurich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-2A, C167Homo sapiensMutation(s): 0 
Gene Names: CASP2 OR ICH1CASP2ICH1NEDD2
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-2B, D105Homo sapiensMutation(s): 0 
Gene Names: CASP2 OR ICH1CASP2ICH1NEDD2
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
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ACETYL-LEU-ASP-GLU-SER-ASJE, F6Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YKR018C
Find proteins for P36114 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36114 
Go to UniProtKB:  P36114
Protein Feature View
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  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.649α = 90
b = 96.583β = 90
c = 97.547γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-26
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2013-07-03
    Changes: Structure summary