9ne4

cryoEM structure of the A-chain of the human OGA-L Catalytic Dimer

spinqualitylabelsall models 9ne4, resolution 2.98Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 9ne4 is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: Electron Microscopy, Resolution 2.98Å Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function OGA_HUMAN Isoform 1: Cleaves GlcNAc but not GalNAc from O-glycosylated proteins. Can use p-nitrophenyl-beta-GlcNAc and 4-methylumbelliferone-GlcNAc as substrates but not p-nitrophenyl-beta-GalNAc or p-nitrophenyl-alpha-GlcNAc (in vitro) (PubMed:11148210). Does not bind acetyl-CoA and does not have histone acetyltransferase activity (PubMed:24088714). Isoform 3: Cleaves GlcNAc but not GalNAc from O-glycosylated proteins. Can use p-nitrophenyl-beta-GlcNAc as substrate but not p-nitrophenyl-beta-GalNAc or p-nitrophenyl-alpha-GlcNAc (in vitro), but has about six times lower specific activity than isoform 1. Publication Abstract from PubMed 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 A, and the locally refined OGA A- and B-chains to 2.98 A and 3.05 A 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(Me3) and H4K(5,8,12,16Ac) modifications. The OGA-L-H3K36(Me3) 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. Human O-GlcNAcase catalytic-stalk dimer anchors flexible histone binding domains.,Nyenhuis SB, Steenackers A, Mukherjee MM, Hinshaw JE, Hanover JA Commun Chem. 2025 Dec 9. doi: 10.1038/s42004-025-01813-7. PMID:41366547 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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