Crystal structure of a clip-domain serine protease and functional roles of the clip domains

EMBO J. 2005 Dec 21;24(24):4404-14. doi: 10.1038/sj.emboj.7600891. Epub 2005 Dec 15.


Clip-domain serine proteases (SPs) are the essential components of extracellular signaling cascades in various biological processes, especially in embryonic development and the innate immune responses of invertebrates. They consist of a chymotrypsin-like SP domain and one or two clip domains at the N-terminus. Prophenoloxidase-activating factor (PPAF)-II, which belongs to the noncatalytic clip-domain SP family, is indispensable for the generation of the active phenoloxidase leading to melanization, a major defense mechanism of insects. Here, the crystal structure of PPAF-II reveals that the clip domain adopts a novel fold containing a central cleft, which is distinct from the structures of defensins with a similar arrangement of cysteine residues. Ensuing studies demonstrated that PPAF-II forms a homo-oligomer upon cleavage by the upstream protease and that the clip domain of PPAF-II functions as a module for binding phenoloxidase through the central cleft, while the clip domain of a catalytically active easter-type SP plays an essential role in the rapid activation of its protease domain.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Baculoviridae / metabolism
  • Catalytic Domain
  • Catechol Oxidase / chemistry
  • Chromatography
  • Chymotrypsin / chemistry
  • Coleoptera
  • Crystallography, X-Ray
  • Drosophila
  • Enzyme Precursors / chemistry
  • Insecta
  • Microscopy, Electron
  • Models, Molecular
  • Molecular Sequence Data
  • Mutation
  • Protein Binding
  • Protein Conformation
  • Protein Structure, Tertiary
  • Recombinant Proteins / chemistry
  • Sequence Homology, Amino Acid
  • Serine Endopeptidases / chemistry*
  • Serine Endopeptidases / metabolism
  • Signal Transduction


  • Enzyme Precursors
  • Recombinant Proteins
  • pro-phenoloxidase
  • Catechol Oxidase
  • Serine Endopeptidases
  • prephenoloxidase-activating enzyme
  • Chymotrypsin

Associated data

  • PDB/2B9L