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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase-2
A, C
167Homo sapiensGene Names: CASP2 (ICH1, NEDD2)
EC: 3.4.22.55
Find proteins for P42575 (Homo sapiens)
Go to Gene View: CASP2
Go to UniProtKB:  P42575
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Caspase-2
B, D
105Homo sapiensGene Names: CASP2 (ICH1, NEDD2)
EC: 3.4.22.55
Find proteins for P42575 (Homo sapiens)
Go to Gene View: CASP2
Go to UniProtKB:  P42575
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ACETYL-LEU-ASP-GLU-SER-ASJ
E, F
6Saccharomyces cerevisiae (strain ATCC 204508 / S288c)N/A
Find proteins for P36114 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36114
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000241
Query on PRD_000241
E,FN-acetyl-L-leucyl-L-alpha-aspartyl-L-alpha-glutamyl-L-seryl-L-aspartic aldehydePeptide-like / Inhibitor

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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 = 90.00
b = 96.583β = 90.00
c = 97.547γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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