2YDR

CpOGA D298N in complex with p53-derived O-GlcNAc peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Synergy of Peptide and Sugar in O-Glcnacase Substrate Recognition.

Schimpl, M.Borodkin, V.S.Gray, L.J.Van Aalten, D.M.F.

(2012) Chem Biol 19: 173

  • DOI: 10.1016/j.chembiol.2012.01.011
  • Primary Citation of Related Structures:  
    2YDQ, 2YDR, 2YDS

  • PubMed Abstract: 
  • Protein O-GlcNAcylation is an essential reversible posttranslational modification in higher eukaryotes. O-GlcNAc addition and removal is catalyzed by O-GlcNAc transferase and O-GlcNAcase, respectively. We report the molecular details of the interaction of a bacterial O-GlcNAcase homolog with three different synthetic glycopeptides derived from characterized O-GlcNAc sites in the human proteome ...

    Protein O-GlcNAcylation is an essential reversible posttranslational modification in higher eukaryotes. O-GlcNAc addition and removal is catalyzed by O-GlcNAc transferase and O-GlcNAcase, respectively. We report the molecular details of the interaction of a bacterial O-GlcNAcase homolog with three different synthetic glycopeptides derived from characterized O-GlcNAc sites in the human proteome. Strikingly, the peptides bind a conserved O-GlcNAcase substrate binding groove with similar orientation and conformation. In addition to extensive contacts with the sugar, O-GlcNAcase recognizes the peptide backbone through hydrophobic interactions and intramolecular hydrogen bonds, while avoiding interactions with the glycopeptide side chains. These findings elucidate the molecular basis of O-GlcNAcase substrate specificity, explaining how a single enzyme achieves cycling of the complete O-GlcNAc proteome. In addition, this work will aid development of O-GlcNAcase inhibitors that target the peptide binding site.


    Organizational Affiliation

    Division of Cell Signalling & Immunology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CELLULAR TUMOR ANTIGEN P53P11Homo sapiensMutation(s): 0 
Gene Names: TP53P53
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
NIH Common Fund Data Resources
PHAROS  P04637
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
O-GLCNACASE NAGJA590Clostridium perfringensMutation(s): 1 
EC: 3.2.1.52 (PDB Primary Data), 3.2.1.169 (UniProt)
Find proteins for Q0TR53 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A))
Explore Q0TR53 
Go to UniProtKB:  Q0TR53
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
P
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CD
Query on CD

Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.95α = 90
b = 117.95β = 90
c = 148.121γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary