Structural basis for histone N-terminal recognition by human peptidylarginine deiminase 4

Abstract

Histone arginine methylation is a posttranslational modification linked to the regulation of gene transcription. Unlike other posttranslational 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 Ca 2؉ -dependent enzyme previously known to convert arginine residues to citrulline in histones, can also convert monomethylated 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 posttranslational modification that regulates the level of histone arginine methylation and gene activity. Here we present the crystal structures of a Ca 2؉ -bound PAD4 mutant in complex with three histone N-terminal peptides, each consisting of 10 amino acid residues that include one target arginine residue for the enzyme (H3͞Arg-8, H3͞Arg-17, and H4͞Arg-3). To each histone N-terminal peptide, the enzyme induces a ␤-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 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.calcium binding ͉ histone modification ͉ rheumatoid arthritis ͉ protein deimination͞citrullination ͉ x-ray crystal structure

Regulation of histone modification and chromatin structure by the p53–PADI4 pathway

“…Although the molecular mechanism of how PADI4 increases DNA accessibility was not fully elucidated, loss of positive charge by citrullination was shown to induce conformational changes of histone H4 N terminal 40 . DNA-histone interaction is chargedependent, and changes in the charge of the histone tails are considered to weaken histone-DNA interaction 41 .…”

Dysregulation of PAD4-mediated citrullination of nuclear GSK3β activates TGF-β signaling and induces epithelial-to-mesenchymal transition in breast cancer cells

“…Given the phenotypic switch in shPAD4 cells, we sought to identify putative targets of PAD4 that might account for induction of the EMT phenotype. Crystallographic data suggest that PAD4 does not recognize specific arginine residues in a unique sequence context but rather recognizes five successive residues with the consensus sequence 1 ϕXRXX 5 , in which ϕ denotes amino acids with small side-chain moieties, and X denotes any amino acid (21). The target sequence must also be accessible and flexible enough to fit into the active pocket of PAD4, much like the N-terminal sequence SGRGK of human histones H4 and H2A, whose arginine at position 3 (R3) is one of the better described targets of PAD4 (14,21,22).…”

“…Crystallographic data suggest that PAD4 does not recognize specific arginine residues in a unique sequence context but rather recognizes five successive residues with the consensus sequence 1 ϕXRXX 5 , in which ϕ denotes amino acids with small side-chain moieties, and X denotes any amino acid (21). The target sequence must also be accessible and flexible enough to fit into the active pocket of PAD4, much like the N-terminal sequence SGRGK of human histones H4 and H2A, whose arginine at position 3 (R3) is one of the better described targets of PAD4 (14,21,22). Because initiating methionines (M) often are removed during protein maturation, we searched the proteome for sequences beginning with an amino (N)-terminal MSGR motif using pBLAST and PredMod (23).…”

Anticancer Peptidylarginine Deiminase (PAD) Inhibitors Regulate the Autophagy Flux and the Mammalian Target of Rapamycin Complex 1 Activity

“…A recent study with PAD2, PAD3, and PAD4 enzymes found that PAD4 prefers histone H3, whereas PAD2 prefers actin for citrullination (11). However, the interaction of PAD4 with its substrate peptides is mainly mediated by the peptide backbone (58), suggesting that PAD4 may target Arg residues embedded in a diverse range of substrates. To date, histones H3, H4, and H2A, ING4, nucleophosmin, and nuclear lamin C have been identified as substrate of PAD4.…”