2DKO

Extended substrate recognition in caspase-3 revealed by high resolution X-ray structure analysis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.142 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Extended Substrate Recognition in Caspase-3 Revealed by High Resolution X-ray Structure Analysis

Ganesan, R.Mittl, P.R.E.Jelakovic, S.Grutter, M.G.

(2006) J Mol Biol 359: 1378-1388

  • DOI: 10.1016/j.jmb.2006.04.051
  • Primary Citation of Related Structures:  
    2CJX, 2CJY, 2DKO

  • PubMed Abstract: 
  • Caspases are cysteine proteases involved in the signalling cascades of programmed cell death in which caspase-3 plays a central role, since it propagates death signals from intrinsic and extrinsic stimuli to downstream targets. The atomic resolution (1.06 Angstroms) crystal structure of the caspase-3 DEVD-cmk complex reveals the structural basis for substrate selectivity in the S4 pocket ...

    Caspases are cysteine proteases involved in the signalling cascades of programmed cell death in which caspase-3 plays a central role, since it propagates death signals from intrinsic and extrinsic stimuli to downstream targets. The atomic resolution (1.06 Angstroms) crystal structure of the caspase-3 DEVD-cmk complex reveals the structural basis for substrate selectivity in the S4 pocket. A low-barrier hydrogen bond is observed between the side-chains of the P4 inhibitor aspartic acid and Asp179 of the N-terminal tail of the symmetry related p12 subunit. Site-directed mutagenesis of Asp179 confirmed the significance of this residue in substrate recognition. In the 1.06 Angstroms crystal structure, a radiation damage induced rearrangement of the inhibitor methylketone moiety was observed. The carbon atom that in a substrate would represent the scissile peptide bond carbonyl carbon clearly shows a tetrahedral coordination and resembles the postulated tetrahedral intermediate of the acylation reaction.


    Organizational Affiliation

    Biochemisches Institut, Universität Zürich, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-3 A146Homo sapiensMutation(s): 0 
Gene Names: CASP3CPP32
EC: 3.4.22 (PDB Primary Data), 3.4.22.56 (UniProt)
Find proteins for P42574 (Homo sapiens)
Explore P42574 
Go to UniProtKB:  P42574
NIH Common Fund Data Resources
PHAROS:  P42574
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-3 B103Homo sapiensMutation(s): 1 
Gene Names: CASP3CPP32
EC: 3.4.22 (PDB Primary Data), 3.4.22.56 (UniProt)
Find proteins for P42574 (Homo sapiens)
Explore P42574 
Go to UniProtKB:  P42574
NIH Common Fund Data Resources
PHAROS:  P42574
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PHQ-ASP-GLU-VAL-ASP-CHLOROMETHYLKETONE I6N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.142 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.65α = 90
b = 83.89β = 90
c = 96.16γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XSCALEdata scaling
AMoREphasing
SHELXL-97refinement
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    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: 2014-04-02
    Changes: Structure summary