Structural basis for executioner caspase recognition of P5 position in substrates

Apoptosis. 2008 Nov;13(11):1291-302. doi: 10.1007/s10495-008-0259-9.


Caspase-3, -6 and -7 cleave many proteins at specific sites to induce apoptosis. Their recognition of the P5 position in substrates has been investigated by kinetics, modeling and crystallography. Caspase-3 and -6 recognize P5 in pentapeptides as shown by enzyme activity data and interactions observed in the crystal structure of caspase-3/LDESD and in a model for caspase-6. In caspase-3 the P5 main-chain was anchored by interactions with Ser209 in loop-3 and the P5 Leu side-chain interacted with Phe250 and Phe252 in loop-4 consistent with 50% increased hydrolysis of LDEVD relative to DEVD. Caspase-6 formed similar interactions and showed a preference for polar P5 in QDEVD likely due to interactions with polar Lys265 and hydrophobic Phe263 in loop-4. Caspase-7 exhibited no preference for P5 residue in agreement with the absence of P5 interactions in the caspase-7/LDESD crystal structure. Initiator caspase-8, with Pro in the P5-anchoring position and no loop-4, had only 20% activity on tested pentapeptides relative to DEVD. Therefore, caspases-3 and -6 bind P5 using critical loop-3 anchoring Ser/Thr and loop-4 side-chain interactions, while caspase-7 and -8 lack P5-binding residues.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Apoptosis*
  • Caspase 3 / chemistry
  • Caspase 6 / chemistry
  • Caspase 7 / chemistry
  • Caspase 8 / chemistry
  • Catalysis
  • Crystallography, X-Ray / methods
  • Cysteine Endopeptidases / chemistry*
  • Humans
  • Molecular Conformation
  • Molecular Sequence Data
  • Peptides / chemistry
  • Sequence Homology, Amino Acid
  • Substrate Specificity


  • Peptides
  • Caspase 3
  • Caspase 6
  • Caspase 7
  • Caspase 8
  • Cysteine Endopeptidases