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 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

Validation slider image for 9QEP

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 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.

Macromolecule Content 

  • Total Structure Weight: 168.19 kDa 
  • Atom Count: 6,942 
  • Modeled Residue Count: 848 
  • Deposited Residue Count: 1,446 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

View Full Validation Report



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