8FUF | pdb_00008fuf

Crystal structure of human O-GlcNAc transferase (OGT) in complex with an exosite-binding peptide (ZNF831) and UDP-GlcNAc

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-01-17 Released: 2023-08-09 
  • Deposition Author(s): Xie, J., Jiang, J.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.69 Å
  • R-Value Free: 
    0.242 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Motif-dependent binding on the intervening domain regulates O-GlcNAc transferase.

Blankenship, C.M.Xie, J.Benz, C.Wang, A.Ivarsson, Y.Jiang, J.

(2023) Nat Chem Biol 19: 1423-1431

  • DOI: https://doi.org/10.1038/s41589-023-01422-2
  • Primary Citation Related Structures: 
    8FE6, 8FE7, 8FUF

  • PubMed Abstract: 

    The modification of intracellular proteins with O-linked β-N-acetylglucosamine (O-GlcNAc) moieties is a highly dynamic process that spatiotemporally regulates nearly every important cellular program. Despite its significance, little is known about the substrate recognition and regulation modes of O-GlcNAc transferase (OGT), the primary enzyme responsible for O-GlcNAc addition. In this study, we identified the intervening domain (Int-D), a poorly understood protein fold found only in metazoan OGTs, as a specific regulator of OGT protein-protein interactions and substrate modification. Using proteomic peptide phage display (ProP-PD) coupled with structural, biochemical and cellular characterizations, we discovered a strongly enriched peptide motif, employed by the Int-D to facilitate specific O-GlcNAcylation. We further show that disruption of Int-D binding dysregulates important cellular programs, including response to nutrient deprivation and glucose metabolism. These findings illustrate a mode of OGT substrate recognition and offer key insights into the biological roles of this unique domain.


  • Organizational Affiliation
    • Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.

Macromolecule Content 

  • Total Structure Weight: 332.52 kDa 
  • Atom Count: 22,492 
  • Modeled Residue Count: 2,824 
  • Deposited Residue Count: 2,944 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
A, C, E, G
723Homo sapiensMutation(s): 0 
Gene Names: OGT
EC: 2.4.1.255
UniProt & NIH Common Fund Data Resources
Find proteins for O15294 (Homo sapiens)
Explore O15294 
Go to UniProtKB:  O15294
PHAROS:  O15294
GTEx:  ENSG00000147162 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15294
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc finger protein 831
B, D, F, H
13Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q5JPB2 (Homo sapiens)
Explore Q5JPB2 
Go to UniProtKB:  Q5JPB2
PHAROS:  Q5JPB2
GTEx:  ENSG00000124203 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JPB2
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.69 Å
  • R-Value Free:  0.242 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 274.011α = 90
b = 274.011β = 90
c = 143.078γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM121718

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-08
    Changes: Database references