6RHE

CpOGA D298N in complex with hOGA-derived S-GlcNAc peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Genetic recoding to dissect the roles of site-specific protein O-GlcNAcylation.

Gorelik, A.Bartual, S.G.Borodkin, V.S.Varghese, J.Ferenbach, A.T.van Aalten, D.M.F.

(2019) Nat.Struct.Mol.Biol. 26: 1071-1077

  • DOI: 10.1038/s41594-019-0325-8

  • PubMed Abstract: 
  • Modification of specific Ser and Thr residues of nucleocytoplasmic proteins with O-GlcNAc, catalyzed by O-GlcNAc transferase (OGT), is an abundant posttranslational event essential for proper animal development and is dysregulated in various diseases ...

    Modification of specific Ser and Thr residues of nucleocytoplasmic proteins with O-GlcNAc, catalyzed by O-GlcNAc transferase (OGT), is an abundant posttranslational event essential for proper animal development and is dysregulated in various diseases. Due to the rapid concurrent removal by the single O-GlcNAcase (OGA), precise functional dissection of site-specific O-GlcNAc modification in vivo is currently not possible without affecting the entire O-GlcNAc proteome. Exploiting the fortuitous promiscuity of OGT, we show that S-GlcNAc is a hydrolytically stable and accurate structural mimic of O-GlcNAc that can be encoded in mammalian systems with CRISPR-Cas9 in an otherwise unperturbed O-GlcNAcome. Using this approach, we target an elusive Ser 405 O-GlcNAc site on OGA, showing that this site-specific modification affects OGA stability.


    Organizational Affiliation

    MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK.,Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.,Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK. dmfvanaalten@dundee.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
O-GlcNAcase NagJ
A
592Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)Mutation(s): 1 
Gene Names: nagJ
EC: 3.2.1.169
Find proteins for Q0TR53 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A))
Go to UniProtKB:  Q0TR53
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ACY-ALA-HIS-CYS-GLY-NH2
D
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A, D
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
D
NON-POLYMERH2 N

--

ACY
Query on ACY
D
NON-POLYMERC2 H4 O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 117.651α = 90.00
b = 117.651β = 90.00
c = 147.900γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom105310/Z/14/Z

Revision History 

  • Version 1.0: 2019-12-25
    Type: Initial release