4GYY

Crystal structure of human O-GlcNAc Transferase with UDP-5SGlcNAc and a peptide substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural snapshots of the reaction coordinate for O-GlcNAc transferase.

Lazarus, M.B.Jiang, J.Gloster, T.M.Zandberg, W.F.Whitworth, G.E.Vocadlo, D.J.Walker, S.

(2012) Nat.Chem.Biol. 8: 966-968

  • DOI: 10.1038/nchembio.1109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Visualization of the reaction coordinate undertaken by glycosyltransferases has remained elusive but is critical for understanding this important class of enzyme. Using substrates and substrate mimics, we describe structural snapshots of all species ...

    Visualization of the reaction coordinate undertaken by glycosyltransferases has remained elusive but is critical for understanding this important class of enzyme. Using substrates and substrate mimics, we describe structural snapshots of all species along the kinetic pathway for human O-linked β-N-acetylglucosamine transferase (O-GlcNAc transferase), an intracellular enzyme that catalyzes installation of a dynamic post-translational modification. The structures reveal key features of the mechanism and show that substrate participation is important during catalysis.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
A, C
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
Casein kinase II subunit alpha
B, D
14Homo sapiensMutation(s): 0 
Gene Names: CSNK2A1 (CK2A1)
EC: 2.7.11.1
Find proteins for P68400 (Homo sapiens)
Go to Gene View: CSNK2A1
Go to UniProtKB:  P68400
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
12V
Query on 12V

Download SDF File 
Download CCD File 
A, C
(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate
URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE
C17 H27 N3 O16 P2 S
JPRVHSQHWXZSNC-UBDZBXRQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.218 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 98.520α = 90.00
b = 136.480β = 103.51
c = 152.770γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
SCALAdata scaling
PHENIXmodel building
PHENIXrefinement
PHENIXphasing
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2012-12-12
    Type: Database references