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 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/nchembio.1108
  • Primary Citation of Related Structures:  

  • 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 reco ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYL TRANSFERASE 110 KDA SUBUNIT
A, B, C, D
723Homo sapiensMutation(s): 0 
Gene Names: OGT
EC: 2.4.1.255
Find proteins for O15294 (Homo sapiens)
Go to Gene View: OGT
Go to UniProtKB:  O15294
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GTAB1TIDE
I, J, K, L
11Homo sapiensMutation(s): 0 
Gene Names: TAB1 (MAP3K7IP1)
Find proteins for Q15750 (Homo sapiens)
Go to Gene View: TAB1
Go to UniProtKB:  Q15750
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP

Download SDF File 
Download CCD File 
A, B, C, D
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
I, J, K, L
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UDPIC50: 1800 nM (100) BINDINGDB
UDPKd: 540 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.174 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 274.170α = 90.00
b = 274.170β = 90.00
c = 142.150γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2012-12-05
    Type: Database references
  • Version 1.2: 2012-12-12
    Type: Database references