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- PDB-9qep: Cryo-EM structure of O-GlcNAcase from Trichoplax Adhaerens -

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Basic information

Entry
Database: PDB / ID: 9qep
TitleCryo-EM structure of O-GlcNAcase from Trichoplax Adhaerens
ComponentsO-GlcNAcase
KeywordsHYDROLASE / GH84 hydrolase
Function / homology
Function and homology information


hexosaminidase activity / protein O-GlcNAcase / [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine/L-threonine O-N-acetyl-alpha-D-glucosaminase activity / carbohydrate derivative metabolic process
Similarity search - Function
Beta-N-acetylglucosaminidase / beta-N-acetylglucosaminidase / Glycosyl hydrolases family 84 (GH84) domain profile. / : / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesTrichoplax adhaerens (invertebrata)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsBasse Hansen, S. / Bartual, S.G. / Yuan, H. / Raimi, O.G. / Gorelik, A. / Ferenbach, A.T. / Lytje, K. / Pedersen, J.S. / Drace, T. / Boesen, T. / van Aalten, D.M.F.
Funding support United Kingdom, Denmark, 2items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.1Oct 15, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: O-GlcNAcase
B: O-GlcNAcase


Theoretical massNumber of molelcules
Total (without water)168,1902
Polymers168,1902
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein O-GlcNAcase


Mass: 84094.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplax adhaerens (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D5X2Y8, protein O-GlcNAcase
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: O-GlcNAcase from Trichoplax Adhaerens (TaOGA) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Trichoplax adhaerens (invertebrata)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 293 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 59.9 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 141300 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047112
ELECTRON MICROSCOPYf_angle_d0.8469608
ELECTRON MICROSCOPYf_dihedral_angle_d15.2442614
ELECTRON MICROSCOPYf_chiral_restr0.0521024
ELECTRON MICROSCOPYf_plane_restr0.0071226

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