|
Prof. Mamoru Sato (Yokohama City University) and coworkers (Dr. Kyouhei Arita, Dr. Toshiyuki Shimizu, Dr. Hiroshi Hashimoto, Dr. Yuji Hidaka, and Prof. Michiyuki Yamada) have determined the crystal structures of human PAD4 (peptidylarginine deiminase 4) in complex with three histone N-terminal peptides, using the Structural Biology III Beamline (BL38B1) of SPring-8 and NW12 of Photon Factory Advanced Ring (PF-AR).
Histone arginine methylation is a post-translational modification linked to the regulation of gene transcription. Unlike other post-translational modifications, methylation has generally been regarded as stable, and enzymes that demethylate histone arginine residues have not been identified. However, it has recently been shown that human peptidylarginine deiminase 4 (PAD4), a Ca2+-dependent enzyme previously known to convert arginine residues to citrulline in histones, can also convert mono-methylated arginine residues to citrulline both in vivo and in vitro. Citrullination of histone arginine residues by the enzyme antagonizes methylation by histone arginine methyltransferases, and is thus a novel post-translational modification that regulates the level of histone arginine methylation and gene activity.
PAD4 also shows deiminating activity dysregulated in rheumatoid arthritis (RA). Specific evidence linking the dysregulation of this enzyme to RA includes:
i) the fact that the PAD4 gene has been identified as a RA-susceptibility locus in the Japanese and Korean population;
ii) PAD4 and citrulline-containing proteins co-localize in RA synovial tissues, and the level of their expression is correlated to the severity of the disease;
iii) the RA-associated Major Histocompatibility Complex II molecule (HLA-DRB1*0401) binds preferentially to citrulline-containing peptides; and
iv) RA patients produce autoantibodies that recognize citrulline-containing peptides and these autoantibodies can often be detected prior to the onset clinical symptoms. It has been suggested that an elevated PAD4 activity causes an overproduction of deiminated proteins that initially leads to a break in self tolerance, and eventually causes the immune system to attack its own tissues.
In the present study, Prof. Mamoru Sato and coworkers determined the crystal structures of a Ca2+-bound PAD4 mutant in complex with three histone N-terminal peptides, each consisting of ten amino-acid residues that include one target arginine residue for the enzyme (H3/Arg-8, H3/Arg-17, and H4/Arg-3). To each histone N-terminal peptide, the enzyme induces a β-turn like bent conformation composed of five successive residues at the molecular surface near the active site cleft. The remaining five residues are highly disordered. The enzyme recognizes each peptide through backbone atoms of the peptide with a possible consensus recognition motif. The sequence specificity of the peptide recognized by this enzyme is thought to be fairly broad.
These observations provide novel structural insights into target protein recognition by histone modification enzymes, and illustrate how PAD4 can target multiple arginine sites in the histone N-terminal tails. The present findings will be very helpful in the elucidation of detailed PAD4-substrate interactions and thereby suggest useful strategies to develop PAD-inhibiting drugs for RA.
Article:
"Structural basis for histone N-terminal recognition by human peptidylarginine deiminase 4"
Kyouhei Arita, Toshiyuki Shimizu, Hiroshi Hashimoto, Yuji Hidaka, Michiyuki Yamada, and Mamoru Sato
Proc. Natl. Acad. Sci. USA., April 4, 2006, Vol. 103, No. 14, 5291-5296
|