5VIE

Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase.

Hu, C.W.Worth, M.Fan, D.Li, B.Li, H.Lu, L.Zhong, X.Lin, Z.Wei, L.Ge, Y.Li, L.Jiang, J.

(2017) Nat. Chem. Biol. 13: 1267-1273

  • DOI: 10.1038/nchembio.2494
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) is an essential human glycosyltransferase that adds O-GlcNAc modifications to numerous proteins. However, little is known about the mechanism with which OGT recognizes various protein substr ...

    O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) is an essential human glycosyltransferase that adds O-GlcNAc modifications to numerous proteins. However, little is known about the mechanism with which OGT recognizes various protein substrates. Here we report on GlcNAc electrophilic probes (GEPs) to expedite the characterization of OGT-substrate recognition. Data from mass spectrometry, X-ray crystallization, and biochemical and radiolabeled kinetic assays support the application of GEPs to rapidly report the impacts of OGT mutations on protein substrate or sugar binding and to discover OGT residues crucial for protein recognition. Interestingly, we found that the same residues on the inner surface of the N-terminal domain contribute to OGT interactions with different protein substrates. By tuning reaction conditions, a GEP enables crosslinking of OGT with acceptor substrates in situ, affording a unique method to discover genuine substrates that weakly or transiently interact with OGT. Hence, GEPs provide new strategies to dissect OGT-substrate binding and recognition.


    Organizational Affiliation

    Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 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
CKII
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9CD
Query on 9CD

Download SDF File 
Download CCD File 
C
2-{[(2E)-but-2-enoyl]amino}-2-deoxy-beta-D-glucopyranose
C10 H17 N O6
GANGCWNSYXFAHD-SUZWSAGVSA-N
 Ligand Interaction
9C1
Query on 9C1

Download SDF File 
Download CCD File 
B
2-{[(2E)-4-chlorobut-2-enoyl]amino}-2-deoxy-beta-D-glucopyranose
C10 H16 Cl N O6
LKECTNVLFDGIBK-KKRTVAFTSA-N
 Ligand Interaction
UDP
Query on UDP

Download SDF File 
Download CCD File 
A, C
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.248 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 138.734α = 90.00
b = 200.025β = 90.00
c = 152.986γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Unviersity of Wisconsin-MadisonUnited States--

Revision History 

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2017-11-08
    Type: Database references
  • Version 1.2: 2017-12-06
    Type: Database references