Structural basis of procaspase-9 recruitment by the apoptotic protease-activating factor 1

Nature. 1999 Jun 10;399(6736):549-57. doi: 10.1038/21124.


Caspase-9-mediated apoptosis (programmed cell death) plays a central role in the development and homeostasis of all multicellular organisms. Mature caspase-9 is derived from its procaspase precursor as a result of recruitment by the activating factor Apaf-1. The crystal structures of the caspase-recruitment domain of Apaf-1 by itself and in complex with the prodomain of procaspase-9 have been determined at 1.6 and 2.5 A resolution, respectively. These structures and other evidence reveal that each molecule of Apaf-1 interacts with a molecule of procaspase-9 through two highly charged and complementary surfaces formed by non-conserved residues; these surfaces determine recognition specificity through networks of intermolecular hydrogen bonds and van der Waals interactions. Mutation of the important interface residues in procaspase-9 or Apaf-1 prevents or reduces activation of procaspase-9 in a cell-free system. Wild-type, but not mutant, prodomains of caspase-9 completely inhibit catalytic processing of procaspase-9. Furthermore, analysis of homologues from Caenorhabditis elegans indicates that recruitment of CED-3 by CED-4 is probably mediated by the same set of conserved structural motifs, with a corresponding change in the specificity-determining residues.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Apoptosis*
  • Apoptotic Protease-Activating Factor 1
  • Binding Sites
  • Caspase 9
  • Caspase Inhibitors
  • Caspases / chemistry*
  • Caspases / genetics
  • Caspases / metabolism
  • Cloning, Molecular
  • Crystallography, X-Ray
  • Enzyme Activation
  • Enzyme Precursors / antagonists & inhibitors
  • Enzyme Precursors / chemistry*
  • Enzyme Precursors / genetics
  • Enzyme Precursors / metabolism
  • Escherichia coli
  • Humans
  • Models, Molecular
  • Molecular Sequence Data
  • Mutagenesis, Site-Directed
  • Point Mutation
  • Protein Binding
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / genetics
  • Proteins / metabolism
  • Recombinant Fusion Proteins / chemistry
  • Recombinant Fusion Proteins / genetics
  • Static Electricity


  • APAF1 protein, human
  • Apoptotic Protease-Activating Factor 1
  • Caspase Inhibitors
  • Enzyme Precursors
  • Proteins
  • Recombinant Fusion Proteins
  • CASP9 protein, human
  • Caspase 9
  • Caspases

Associated data

  • PDB/2YGS
  • PDB/3YGS