5C1D

Human OGT in complex with UDP-5S-GlcNAc and substrate peptide (RB2L)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

The active site of O-GlcNAc transferase imposes constraints on substrate sequence.

Pathak, S., Alonso, J., Schimpl, M., Rafie, K., Blair, D.E., Borodkin, V.S., Schuttelkopf, A.W., Albarbarawi, O., van Aalten, D.M.

(2015) Nat Struct Mol Biol 22: 744-750

  • DOI: 10.1038/nsmb.3063
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • O-GlcNAc transferase (OGT) glycosylates a diverse range of intracellular proteins with O-linked N-acetylglucosamine (O-GlcNAc), an essential and dynamic post-translational modification in metazoans. Although this enzyme modifies hundreds of proteins ...

    O-GlcNAc transferase (OGT) glycosylates a diverse range of intracellular proteins with O-linked N-acetylglucosamine (O-GlcNAc), an essential and dynamic post-translational modification in metazoans. Although this enzyme modifies hundreds of proteins with O-GlcNAc, it is not understood how OGT achieves substrate specificity. In this study, we describe the application of a high-throughput OGT assay to a library of peptides. We mapped sites of O-GlcNAc modification by electron transfer dissociation MS and found that they correlate with previously detected O-GlcNAc sites. Crystal structures of four acceptor peptides in complex with Homo sapiens OGT suggest that a combination of size and conformational restriction defines sequence specificity in the -3 to +2 subsites. This work reveals that although the N-terminal TPR repeats of OGT may have roles in substrate recognition, the sequence restriction imposed by the peptide-binding site makes a substantial contribution to O-GlcNAc site specificity.

    Organizational Affiliation: 

    Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, UK.



Macromolecules
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Retinoblastoma-like protein 2
C
8Homo sapiensMutation(s): 0 
Gene Names: RBL2, RB2
Find proteins for Q08999 (Homo sapiens)
Go to UniProtKB:  Q08999
NIH Common Fund Data Resources
PHAROS  Q08999
GTEx  ENSG00000103479
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
A
723Homo sapiensMutation(s): 0 
Gene Names: OGT
EC: 2.4.1.255
Find proteins for O15294 (Homo sapiens)
Go to UniProtKB:  O15294
NIH Common Fund Data Resources
PHAROS  O15294
GTEx  ENSG00000147162
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
12V
Query on 12V
Download CCD File 
A
(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
C17 H27 N3 O16 P2 S
JPRVHSQHWXZSNC-UBDZBXRQSA-N		 Ligand Interaction
PO4
Query on PO4
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.527α = 90
b = 151.611β = 90
c = 200.429γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2015-09-16
    Changes: Database references