3R6G

Crystal structure of active caspase-2 bound with Ac-VDVAD-CHO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and enzymatic insights into caspase-2 protein substrate recognition and catalysis.

Tang, Y.Wells, J.A.Arkin, M.R.

(2011) J.Biol.Chem. 286: 34147-34154

  • DOI: 10.1074/jbc.M111.247627
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Caspase-2, the most evolutionarily conserved member in the human caspase family, may play important roles in stress-induced apoptosis, cell cycle regulation, and tumor suppression. In biochemical assays, caspase-2 uniquely prefers a pentapeptide (suc ...

    Caspase-2, the most evolutionarily conserved member in the human caspase family, may play important roles in stress-induced apoptosis, cell cycle regulation, and tumor suppression. In biochemical assays, caspase-2 uniquely prefers a pentapeptide (such as VDVAD) rather than a tetrapeptide, as required for efficient cleavage by other caspases. We investigated the molecular basis for pentapeptide specificity using peptide analog inhibitors and substrates that vary at the P5 position. We determined the crystal structures of apo caspase-2, caspase-2 in complex with peptide inhibitors VDVAD-CHO, ADVAD-CHO, and DVAD-CHO, and a T380A mutant of caspase-2 in complex with VDVAD-CHO. Two residues, Thr-380 and Tyr-420, are identified to be critical for the P5 residue recognition; mutation of the two residues reduces the catalytic efficiency by about 4- and 40-fold, respectively. The structures also provide a series of snapshots of caspase-2 in different catalytic states, shedding light on the mechanism of capase-2 activation, substrate binding, and catalysis. By comparing the apo and inhibited caspase-2 structures, we propose that the disruption of a non-conserved salt bridge between Glu-217 and the invariant Arg-378 is important for the activation of caspase-2. These findings broaden our understanding of caspase-2 substrate specificity and catalysis.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, California 94158, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Caspase-2 subunit p18
A, C
160Homo sapiensMutation(s): 0 
Gene 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 subunit p12
B, D
112Homo sapiensMutation(s): 0 
Gene 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
Peptide Inhibitor (ACE)VDVAD-CHO
F, E
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001048
Query on PRD_001048
E,FN-acetyl-L-valyl-L-alpha-aspartyl-L-valyl-N-[(2R)-1-carboxy-3-oxopropan-2-yl]-L-alaninamidePeptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.322α = 90.00
b = 97.692β = 90.00
c = 96.856γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
Blu-Icedata collection
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-27
    Type: Initial release
  • Version 1.1: 2011-10-19
    Type: Database references
  • Version 1.2: 2012-12-12
    Type: Other