9QEP | pdb_00009qep

Cryo-EM structure of O-GlcNAcase from Trichoplax Adhaerens


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Multi-domain O-GlcNAcase structures reveal allosteric regulatory mechanisms.

Hansen, S.B.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.

(2025) Nat Commun 16: 8828-8828

  • DOI: https://doi.org/10.1038/s41467-025-63893-2
  • Primary Citation of Related Structures:  
    9QEN, 9QEP

  • PubMed 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 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.


  • Organizational Affiliation
    • Section for Neurobiology and DANDRITE, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
O-GlcNAcase
A, B
723Trichoplax adhaerensMutation(s): 0 
EC: 3.2.1.169
UniProt
Find proteins for A0A0D5X2Y8 (Trichoplax adhaerens)
Explore A0A0D5X2Y8 
Go to UniProtKB:  A0A0D5X2Y8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D5X2Y8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.99 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom110061
Novo Nordisk FoundationDenmarkNNF21OC0065969

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release
  • Version 1.1: 2025-10-15
    Changes: Data collection, Database references