Structural basis for Ca(2+)-induced activation of human PAD4

Nat Struct Mol Biol. 2004 Aug;11(8):777-83. doi: 10.1038/nsmb799. Epub 2004 Jul 11.


Peptidylarginine deiminase 4 (PAD4) is a Ca(2+)-dependent enzyme that catalyzes the conversion of protein arginine residues to citrulline. Its gene is a susceptibility locus for rheumatoid arthritis. Here we present the crystal structure of Ca(2+)-free wild-type PAD4, which shows that the polypeptide chain adopts an elongated fold in which the N-terminal domain forms two immunoglobulin-like subdomains, and the C-terminal domain forms an alpha/beta propeller structure. Five Ca(2+)-binding sites, none of which adopt an EF-hand motif, were identified in the structure of a Ca(2+)-bound inactive mutant with and without bound substrate. These structural data indicate that Ca(2+) binding induces conformational changes that generate the active site cleft. Our findings identify a novel mechanism for enzyme activation by Ca(2+) ions, and are important for understanding the mechanism of protein citrullination and for developing PAD-inhibiting drugs for the treatment of rheumatoid arthritis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Arginine / chemistry
  • Binding Sites
  • Cadmium / chemistry
  • Calcium / chemistry*
  • Calcium / metabolism
  • Catalysis
  • Citrulline / chemistry
  • Crystallography, X-Ray
  • Enzyme Activation
  • Humans
  • Hydrolases / chemistry*
  • Hydrolases / metabolism
  • Hydrolysis
  • Ions
  • Models, Chemical
  • Models, Molecular
  • Mutagenesis
  • Mutation
  • Polymorphism, Single Nucleotide
  • Protein Binding
  • Protein Conformation
  • Protein Folding
  • Protein Structure, Tertiary
  • Protein-Arginine Deiminase Type 4
  • Protein-Arginine Deiminases
  • Substrate Specificity


  • Ions
  • Cadmium
  • Citrulline
  • Arginine
  • Hydrolases
  • PADI4 protein, human
  • Protein-Arginine Deiminase Type 4
  • Protein-Arginine Deiminases
  • Calcium

Associated data

  • PDB/1WD8
  • PDB/1WD9
  • PDB/1WDA