PHD finger of the SUMO ligase Siz/PIAS family in rice reveals specific binding for methylated histone H3 at lysine 4 and arginine 2

► We determined the structure of PHD in a rice SUMO ligase Siz1 (OsSiz1–PHD) by NMR. ► OsSiz1–PHD primarily recognizes dimethylated Arg2 of histone H3. ► Methylations at Arg2 and Lys4 of H3 show synergy effect on binding to OsSiz1–PHD. ► 3D NMR models of H3K4me3- and H3R2me2a–OsSiz1–PHD complexes are presented. ► PHD could collaborate with the N-terminal SAP on OsSiz1 binding to chromatin. We determined the three-dimensional structure of the PHD finger of the rice Siz/PIAS-type SUMO ligase, OsSiz1, by NMR spectroscopy and investigated binding ability for a variety of methylated histone H3 tails, showing that OsSiz1–PHD primarily recognizes dimethylated Arg2 of the histone H3 and that methylations at Arg2 and Lys4 reveal synergy effect on binding to OsSiz1–PHD. The K4 cage of OsSiz1–PHD for trimethylated Lys4 of H3K4me3 was similar to that of the BPTF–PHD finger, while the R2 pocket for Arg2 was different. It is intriguing that the PHD module of Siz/PIAS plays an important role, with collaboration with the DNA binding domain SAP, in gene regulation through SUMOylation of a variety of effectors associated with the methylated arginine-riched chromatin domains.