2VSN

Structure and topological arrangement of an O-GlcNAc transferase homolog: insight into molecular control of intracellular glycosylation

• PDB DOI: https://doi.org/10.2210/pdb2VSN/pdb

• Classification: TRANSFERASE
• Organism(s): Xanthomonas campestris pv. campestris str. 8004
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2008-04-28 Released: 2008-06-10 
• Deposition Author(s): Martinez-Fleites, C., Macauley, M.S., He, Y., Shen, D., Vocadlo, D., Davies, G.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.265 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 

Literature

Structure of an O-Glcnac Transferase Homolog Provides Insight Into Intracellular Glycosylation.

Martinez-Fleites, C., Macauley, M.S., He, Y., Shen, D.L., Vocadlo, D.J., Davies, G.J.

(2008) Nat Struct Mol Biol 15: 764

• PubMed: 18536723 
• DOI: https://doi.org/10.1038/nsmb.1443
• Primary Citation of Related Structures:  
  2VSN


• PubMed Abstract: 
  

  N-Acetylglucosamine (O-GlcNAc) modification of proteins provides a mechanism for the control of diverse cellular processes through a dynamic interplay with phosphorylation. UDP-GlcNAc:polypeptidyl transferase (OGT) catalyzes O-GlcNAc addition. The structure of an intact OGT homolog and kinetic analysis of human OGT variants reveal a contiguous superhelical groove that directs substrates to the active site.

---

Organizational Affiliation: 

Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5YW, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 123.49 kDa 
• Atom Count: 8,234 
• Modelled Residue Count: 1,068 
• Deposited Residue Count: 1,136 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XCOGT	A, B	568	Xanthomonas campestris pv. campestris str. 8004	Mutation(s): 1  EC: 2.4 (PDB Primary Data), 2.4.1.255 (UniProt)
UniProt
Find proteins for A0A0H2XAK3 (Xanthomonas campestris pv. campestris (strain 8004)) Explore A0A0H2XAK3  Go to UniProtKB:  A0A0H2XAK3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP	C [auth A], D [auth B]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.265 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.691	α = 90
b = 105.692	β = 90
c = 151.036	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-10 
Deposition Author(s): Martinez-Fleites, C., Macauley, M.S., He, Y., Shen, D., Vocadlo, D., Davies, G.J.

Revision History  

• Version 1.0: 2008-06-10
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other