Human O-GlcNAcase catalytic-stalk dimer anchors flexible histone binding domains

O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA) perform essential functions in signaling, epigenetics, and transcription. Although thousands of proteins are specifically O-GlcNAc modified, the molecular features recognized by the enzymes of O-GlcNAc cycling remain poorly defined. Here we solved the structure of the long isoform of human OGA by cryo-electron microscopy providing a physiologically relevant platform to study the enzyme. The 3.63 Å structure of the dimeric catalytic-stalk dimer differs notably from existing crystal structures. Intriguingly, a low-resolution structure of the OGA-L exhibit densities corresponding to the C-terminal pseudo-HAT domains suggesting substantial flexion of these domains relative to the catalytic-stalk dimer. To explore the role of these domains we found that OGA-L binds to a small subset of the 384 modified histone tails on a commercial array. High specificity binding was observed with modified histone H3K36 peptides, and H4 acetylated peptides. Based on these findings, we propose OGA-L is poised to bind two modified histone tails of nucleosomes in open chromatin but excluded from repressive chromatin. Increased local concentration and activation of OGA-L coupled with its intrinsic conformational flexibility facilitates the removal of O-GlcNAc from target proteins in proximity such as the intrinsically disordered CTD domain of RNA Polymerase II. This model is consistent with OGA-L acting as a ‘reader’ of histone modifications linked to development, transcriptional activation, transposon silencing, and DNA damage repair.