1F9E

CASPASE-8 SPECIFICITY PROBED AT SUBSITE S4: CRYSTAL STRUCTURE OF THE CASPASE-8-Z-DEVD-CHO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Caspase-8 specificity probed at subsite S(4): crystal structure of the caspase-8-Z-DEVD-cho complex.

Blanchard, H.Donepudi, M.Tschopp, M.Kodandapani, L.Wu, J.C.Grutter, M.G.

(2000) J Mol Biol 302: 9-16

  • DOI: 10.1006/jmbi.2000.4041
  • Primary Citation of Related Structures:  
    1F9E

  • PubMed Abstract: 
  • Caspase-8 is an initiator enzyme in the Fas-mediated pathway of which the downstream executioner caspase-3 is a physiological target. Caspases are cysteine proteases that are specific for substrates with an aspartic acid residue at the P(1) position and have an optimal recognition motif that incorporates four amino acid residues N-terminal to the cleavage site ...

    Caspase-8 is an initiator enzyme in the Fas-mediated pathway of which the downstream executioner caspase-3 is a physiological target. Caspases are cysteine proteases that are specific for substrates with an aspartic acid residue at the P(1) position and have an optimal recognition motif that incorporates four amino acid residues N-terminal to the cleavage site. Caspase-8 has been classified as a group III caspase member because it shows a preference for a small hydrophobic residue at the P(4) substrate position. We report the X-ray crystallographic structure of caspase-8 in complex with benzyloxycarbonyl-Asp-Glu-Val-Asp-aldehyde (Z-DEVD), a specific group II caspase inhibitor. The structure shows that the inhibitor interacts favourably with the enzyme in subsite S(4). Kinetic data reveal that Z-DEVD (K(i) 2 nM) is an almost equally potent inhibitor of caspase-8 as the specific group III inhibitor Boc-IETD-aldehyde (K(i) 1 nM). In view of this finding, the original classification of caspases into three specificity groups needs to be modified, at least for caspase-8, which tolerates small hydrophobic residues as well as the acidic residue Asp in subsite S(4). We propose that the subsite S(3) must be considered as an important specificity-determining factor.


    Related Citations: 
    • The three-dimensional structure of caspase-8: an initiator enzyme in apoptosis
      Blanchard, H., Kodandapani, L., Mittl, P.R.E., Marco, S.D., Krebs, J.F., Wu, J.C., Tomaselli, K.J., Gruetter, M.G.
      (1999) Structure 7: 1125
    • The atomic-resolution of human caspase-8, a key activator of apoptosis.
      Watt, W., Koeplinger, K.A., Mildner, A.M., Heinrikson, R.L., Tomasselli, A.G., Watenpaugh, K.D.
      (1999) Structure 7: 1135

    Organizational Affiliation

    Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, Zürich, CH-8057, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CASPASE-8 ALPHA CHAINA, D [auth C], G [auth E], J [auth G], M [auth I], P [auth K]153Homo sapiensMutation(s): 0 
Gene Names: CASP8MCH5
EC: 3.4.22 (PDB Primary Data), 3.4.22.61 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14790 (Homo sapiens)
Explore Q14790 
Go to UniProtKB:  Q14790
PHAROS:  Q14790
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CASPASE-8 BETA CHAINB, E [auth D], H [auth F], K [auth H], N [auth J], Q [auth L]89Homo sapiensMutation(s): 0 
Gene Names: CASP8MCH5
EC: 3.4.22.61
UniProt & NIH Common Fund Data Resources
Find proteins for Q14790 (Homo sapiens)
Explore Q14790 
Go to UniProtKB:  Q14790
PHAROS:  Q14790
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
(PHQ)DEVDC [auth Q], F [auth R], I [auth S], L [auth T], O [auth U], R [auth V]5N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ASA
Query on ASA
C [auth Q], F [auth R], I [auth S], L [auth T], O [auth U], R [auth V]L-PEPTIDE LINKINGC4 H7 N O3ASP
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000331
Query on PRD_000331
C [auth Q], F [auth R], I [auth S], L [auth T], O [auth U], R [auth V]N-[(benzyloxy)carbonyl]-L-alpha-aspartyl-L-alpha-glutamyl-L-valyl-L-aspartic acidPeptide-like /  Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.241 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.029α = 90
b = 188.748β = 90
c = 209.802γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-07-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    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: 2018-01-24
    Changes: Database references