4AY5

Human O-GlcNAc transferase (OGT) in complex with UDP and glycopeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 
    0.204 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UDPClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

O-Glcnac Transferase Invokes Nucleotide Sugar Pyrophosphate Participation in Catalysis

Schimpl, M.Zheng, X.Borodkin, V.S.Blair, D.E.Ferenbach, A.T.Schuettelkopf, A.W.Navratilova, I.Aristotelous, T.Albarbarawi, O.Robinson, D.A.Macnaughtan, M.A.Van Aalten, D.M.F.

(2012) Nat Chem Biol 8: 969

  • DOI: https://doi.org/10.1038/nchembio.1108
  • Primary Citation of Related Structures:  
    4AY5, 4AY6

  • PubMed Abstract: 

    Protein O-GlcNAcylation is an essential post-translational modification on hundreds of intracellular proteins in metazoa, catalyzed by O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) using unknown mechanisms of transfer and substrate recognition. Through crystallographic snapshots and mechanism-inspired chemical probes, we define how human OGT recognizes the sugar donor and acceptor peptide and uses a new catalytic mechanism of glycosyl transfer, involving the sugar donor α-phosphate as the catalytic base as well as an essential lysine. This mechanism seems to be a unique evolutionary solution to the spatial constraints imposed by a bulky protein acceptor substrate and explains the unexpected specificity of a recently reported metabolic OGT inhibitor.


  • Organizational Affiliation

    College of Life Sciences, University of Dundee, Dundee, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYL TRANSFERASE 110 KDA SUBUNIT
A, B, C, D
723Homo sapiensMutation(s): 0 
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
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTAB1TIDEE [auth I],
F [auth J],
G [auth K],
H [auth L]
11synthetic constructMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15750 (Homo sapiens)
Explore Q15750 
Go to UniProtKB:  Q15750
PHAROS:  Q15750
GTEx:  ENSG00000100324 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15750
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q15750-1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

Download Ideal Coordinates CCD File 
I [auth A],
J [auth B],
K [auth C],
L [auth D]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
M [auth I],
N [auth J],
O [auth K],
P [auth L]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
UDP BindingDB:  4AY5 IC50: 1800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free:  0.204 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 274.17α = 90
b = 274.17β = 90
c = 142.15γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted UDPClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2012-12-05
    Changes: Database references
  • Version 1.2: 2012-12-12
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2024-11-13
    Changes: Data collection, Database references, Structure summary