6RHE | pdb_00006rhe

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.233 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

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 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.

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Organizational Affiliation: 
• Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.
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. [e-mail].

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 
• Modeled 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

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 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

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.

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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
• Version 2.2: 2024-10-16
  Changes: Structure summary