3TAX

A Neutral Diphosphate Mimic Crosslinks the Active Site of Human O-GlcNAc Transferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A neutral diphosphate mimic crosslinks the active site of human O-GlcNAc transferase.

Jiang, J.Lazarus, M.B.Pasquina, L.Sliz, P.Walker, S.

(2011) Nat Chem Biol 8: 72-77

  • DOI: 10.1038/nchembio.711
  • Primary Citation of Related Structures:  
    3TAX

  • PubMed Abstract: 
  • Glycosyltransferases (Gtfs) catalyze the formation of a diverse array of glycoconjugates. Small-molecule inhibitors to manipulate Gtf activity in cells have long been sought as tools for understanding Gtf function. Success has been limited because of challenges in designing inhibitors that mimic the negatively charged diphosphate substrates ...

    Glycosyltransferases (Gtfs) catalyze the formation of a diverse array of glycoconjugates. Small-molecule inhibitors to manipulate Gtf activity in cells have long been sought as tools for understanding Gtf function. Success has been limited because of challenges in designing inhibitors that mimic the negatively charged diphosphate substrates. Here we report the mechanism of action of a small molecule that inhibits O-linked N-acetylglucosamine transferase (OGT), an essential human enzyme that modulates cell signaling pathways by catalyzing a unique intracellular post-translational modification, β-O-GlcNAcylation. The molecule contains a five-heteroatom dicarbamate core that functions as a neutral diphosphate mimic. One dicarbamate carbonyl reacts with an essential active site lysine that anchors the diphosphate of the nucleotide-sugar substrate. A nearby cysteine then reacts with the lysine adduct to form a carbonyl crosslink in the OGT active site. Though this unprecedented double-displacement mechanism reflects the unique architecture of the OGT active site, related dicarbamate scaffolds may inhibit other enzymes that bind nucleotide-containing substrates.


    Organizational Affiliation

    Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunitA, C723Homo sapiensMutation(s): 0 
Gene Names: OGT
EC: 2.4.1 (PDB Primary Data), 2.4.1.255 (UniProt)
Find proteins for O15294 (Homo sapiens)
Explore O15294 
Go to UniProtKB:  O15294
NIH Common Fund Data Resources
PHAROS:  O15294
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Casein kinase II subunit alphaB, D14Homo sapiensMutation(s): 0 
Gene Names: CSNK2A1CK2A1
EC: 2.7.11.1
Find proteins for P68400 (Homo sapiens)
Explore P68400 
Go to UniProtKB:  P68400
NIH Common Fund Data Resources
PHAROS:  P68400
Protein Feature View
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  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UDPIC50:  1800   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.6α = 90
b = 136.64β = 103.02
c = 153.319γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
BUSTERrefinement
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-16
    Type: Initial release
  • Version 1.1: 2011-12-28
    Changes: Database references