6RHE

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

• PDB DOI: https://doi.org/10.2210/pdb6RHE/pdb

• Classification: HYDROLASE
• Organism(s): Clostridium perfringens ATCC 13124, Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2019-04-19 Released: 2019-12-25 
• Deposition Author(s): Van Aalten, D., Bartual, S.G., Gorelik, A.
• Funding Organization(s): Wellcome Trust

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.233 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Starting Model: experimental

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

• PubMed: 31695185 
• DOI: https://doi.org/10.1038/s41594-019-0325-8
• Primary Citation of Related Structures:  
  6RHE


• 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. 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: 

Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 69.79 kDa 
• Atom Count: 4,690 
• Modelled Residue Count: 587 
• Deposited Residue Count: 598 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-GlcNAcase NagJ	A	592	Clostridium perfringens ATCC 13124	Mutation(s): 1  Gene Names: nagJ, CPF_1442 EC: 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-ALA-HIS-CYS-GLY-NH2	B [auth D]	6	Homo sapiens	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CD	BA [auth D], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.233 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.651	α = 90
b = 117.651	β = 90
c = 147.9	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Van Aalten, D., Bartual, S.G., Gorelik, A.

---

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	105310/Z/14/Z

Revision History  

• Version 1.0: 2019-12-25
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 2.0: 2023-03-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2024-02-07
  Changes: Data collection, Refinement description