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- EMDB-53081: Cryo-EM structure of human O-GlcNAcase -

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Basic information

Entry
Database: EMDB / ID: EMD-53081
TitleCryo-EM structure of human O-GlcNAcase
Map data
Sample
  • Complex: O-GlcNAcase from Trichoplax Adhaerens (TaOGA)
    • Protein or peptide: Protein O-GlcNAcase
KeywordsGH84 hydrolase / HYDROLASE
Function / homology
Function and homology information


glycoprotein metabolic process / hyalurononglucosaminidase activity / N-acetylglucosamine metabolic process / protein deglycosylation / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / glycoprotein catabolic process / protein O-linked glycosylation / beta-N-acetylglucosaminidase activity / identical protein binding ...glycoprotein metabolic process / hyalurononglucosaminidase activity / N-acetylglucosamine metabolic process / protein deglycosylation / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / glycoprotein catabolic process / protein O-linked glycosylation / beta-N-acetylglucosaminidase activity / identical protein binding / nucleus / membrane / cytosol
Similarity search - Function
Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Acyl-CoA N-acyltransferase / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesTrichoplax adhaerens (invertebrata) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsBasse Hansen S / Bartual SG / Yuan H / Raimi OG / Gorelik A / Ferenbach AT / Lytje K / Pedersen JS / Drace T / Boesen T / van Aalten DMF
Funding support United Kingdom, Denmark, 2 items
OrganizationGrant numberCountry
Wellcome Trust110061 United Kingdom
Novo Nordisk FoundationNNF21OC0065969 Denmark
CitationJournal: Nat Commun / Year: 2025
Title: Multi-domain O-GlcNAcase structures reveal allosteric regulatory mechanisms.
Authors: Sara Basse Hansen / Sergio G Bartual / Huijie Yuan / Olawale G Raimi / Andrii Gorelik / Andrew T Ferenbach / Kristian Lytje / Jan Skov Pedersen / Taner Drace / Thomas Boesen / Daan M F van Aalten /
Abstract: Nucleocytoplasmic protein O-GlcNAcylation is a dynamic modification catalysed by O-GlcNAc transferase (OGT) and reversed by O-GlcNAc hydrolase (OGA), whose activities are regulated through largely ...Nucleocytoplasmic protein O-GlcNAcylation is a dynamic modification catalysed by O-GlcNAc transferase (OGT) and reversed by O-GlcNAc hydrolase (OGA), whose activities are regulated through largely unknown O-GlcNAc-dependent feedback mechanisms. OGA is a homodimeric, multi-domain enzyme containing a catalytic core and a pseudo-histone acetyltransferase (pHAT) domain. While a catalytic structure has been reported, the structure and function of the pHAT domain remain elusive. Here, we report a crystal structure of the Trichoplax adhaerens pHAT domain and cryo-EM data of the multi-domain T. adhaerens and human OGAs, complemented by biophysical analyses. Here, we show that the eukaryotic OGA pHAT domain forms catalytically incompetent, symmetric homodimers, projecting a partially conserved putative peptide-binding site. In solution, OGA exist as flexible multi-domain dimers, but catalytic core-pHAT linker interactions restrict pHAT positional range. In human OGA, pHAT movements remodel the active site environment through conformational changes in a flexible arm region. These findings reveal allosteric mechanisms through which the pHAT domain contributes to O-GlcNAc homeostasis.
History
DepositionMar 10, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53081.png

Downloads & links

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Map

FileDownload / File: emd_53081.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 360 pix.
= 310.56 Å		0.86 Å/pix.
x 360 pix.
= 310.56 Å		0.86 Å/pix.
x 360 pix.
= 310.56 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86267 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.18449263 - 0.39165747
Average (Standard dev.)0.00046454993 (±0.0069166613)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 310.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53081_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53081_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : O-GlcNAcase from Trichoplax Adhaerens (TaOGA)

EntireName: O-GlcNAcase from Trichoplax Adhaerens (TaOGA)
Components
  • Complex: O-GlcNAcase from Trichoplax Adhaerens (TaOGA)
    • Protein or peptide: Protein O-GlcNAcase

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Supramolecule #1: O-GlcNAcase from Trichoplax Adhaerens (TaOGA)

SupramoleculeName: O-GlcNAcase from Trichoplax Adhaerens (TaOGA) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Trichoplax adhaerens (invertebrata)

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Macromolecule #1: Protein O-GlcNAcase

MacromoleculeName: Protein O-GlcNAcase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: protein O-GlcNAcase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 88.206367 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSEERES ELSSNPAASA GASLEPPAAP APGEDNPAGA GGAAVAGAAG GARRFLCGVV EGFYGRPWVM EQRKELFRRL QKWELNTYL YAPKDDYKHR MFWREMYSVE EAEQLMTLIS AAREYEIEFI YAISPGLDIT FSNPKEVSTL KRKLDQVSQF G CRSFALLF ...String:
GPLGSEERES ELSSNPAASA GASLEPPAAP APGEDNPAGA GGAAVAGAAG GARRFLCGVV EGFYGRPWVM EQRKELFRRL QKWELNTYL YAPKDDYKHR MFWREMYSVE EAEQLMTLIS AAREYEIEFI YAISPGLDIT FSNPKEVSTL KRKLDQVSQF G CRSFALLF DDIDHNMCAA DKEVFSSFAH AQVSITNEIY QYLGEPETFL FCPTEYCGTF CYPNVSQSPY LRTVGEKLLP GI EVLWTGP KVVSKEIPVE SIEEVSKIIK RAPVIWDNIH ANDYDQKRLF LGPYKGRSTE LIPRLKGVLT NPNCEFEANY VAI HTLATW YKSNMNGVRK DVVMTDSEDS TVSIQIKLEN EGSDEDIETD VLYSPQMALK LALTEWLQEF GVPHQYSSRQ VAHS GAKAS VVDGTPLVAA GGGGSGGGGS VTLEDLQLLA DLFYLPYEHG PKGAQMLREF QWLRANSSVV SVNCKGKDSE KIEEW RSRA AKFEEMCGLV MGMFTRLSNC ANRTILYDMY SYVWDIKSIM SMVKSFVQWL GCRSHSSAQF LIGDQEPWAF RGGLAG EFQ RLLPIDGAND LFFQPPPLTP TSKVYTIRPY FPKDEASVYK ICREMYDDGV GLPFQSQPDL IGDKLVGGLL SLSLDYC FV LEDEDGICGY ALGTVDVTPF IKKCKISWIP FMQEKYTKPN GDKELSEAEK IMLSFHEEQE VLPETFLANF PSLIKMDI H KKVTDPSVAK SMMACLLSSL KANGSRGAFC EVRPDDKRIL EFYSKLGCFE IAKMEGFPKD VVILGRSL

UniProtKB: Protein O-GlcNAcase, Protein O-GlcNAcase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 99 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 59.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AlphaFold3 predicted model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 140754
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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