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TitleHuman O-GlcNAcase catalytic-stalk dimer anchors flexible histone binding domains.
Journal, issue, pagesCommun Chem, Vol. 9, Issue 1, Page 8, Year 2025
Publish dateDec 9, 2025
AuthorsSarah B Nyenhuis / Agata Steenackers / Mana Mohan Mukherjee / Jenny E Hinshaw / John A Hanover /
PubMed AbstractAlthough thousands of proteins are specifically O-GlcNAc modified, the molecular features recognized by the enzymes of O-GlcNAc cycling (OGT/OGA) remain poorly defined. Here we solved the structure ...Although thousands of proteins are specifically O-GlcNAc modified, the molecular features recognized by the enzymes of O-GlcNAc cycling (OGT/OGA) remain poorly defined. Here we solved the structure of the long isoform of human OGA (OGA-L) by cryo-electron microscopy (cryo-EM) providing a physiologically relevant platform to study the enzyme. The catalytic-stalk dimer structure was solved to a resolution of 3.63 Å, and the locally refined OGA A- and B-chains to 2.98 Å and 3.05 Å respectively. Intriguingly, the cryo-EM structures also exhibit lower resolution densities associated with the pHAT domains, suggesting substantial flexion of these domains relative to the catalytic-stalk dimer. OGA-L binds to a small subset of the 384 modified histone tails on a commercial histone peptide array. High affinity binding of OGA-L was detected to recombinant DNA-containing mononucleosomes bearing the H3K36 and H4K modifications. The OGA-L-H3K36 interaction was further validated by traditional ChIP experiments in MEFs. Thus, OGA-L binds to two modified histone tails of nucleosomes linked to open chromatin, whereas it does not bind to marks associated with repressive chromatin. 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.
External linksCommun Chem / PubMed:41366547 / PubMed Central
MethodsEM (single particle)
Resolution2.98 - 10.07 Å
Structure data

49293

9ne2

EMDB-49293, PDB-9ne2:
cryoEM structure of the human OGA-L Catalytic Dimer
Method: EM (single particle) / Resolution: 3.63 Å

49294

9ne4

EMDB-49294, PDB-9ne4:
cryoEM structure of the A-chain of the human OGA-L Catalytic Dimer
Method: EM (single particle) / Resolution: 2.98 Å

49295

9ne5

EMDB-49295, PDB-9ne5:
cryoEM structure of the B-chain of the human OGA-L Catalytic Dimer
Method: EM (single particle) / Resolution: 3.05 Å

EMDB-49296: cryoEM structure of the human OGA-L Dimer
Method: EM (single particle) / Resolution: 10.07 Å

EMDB-49297: cryoEM structure of the human OGA-L Catalytic Dimer, extra A-chain density
Method: EM (single particle) / Resolution: 3.86 Å

Source
  • homo sapiens (human)
KeywordsHYDROLASE / O-GlcNAC / Histones / DNA repair / DNA Damage / Transcription / Epigenetics

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