Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 87.05 kDa 
• Atom Count: 5596 
• Modelled Residue Count: 756 
• Deposited Residue Count: 776 
• Unique protein chains: 1

1W3B

The superhelical TPR domain of O-linked GlcNAc transferase reveals structural similarities to importin alpha.

• PDB DOI: 10.2210/pdb1W3B/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-07-14 Released: 2004-09-09 
• Deposition Author(s): Jinek, M., Rehwinkel, J., Lazarus, B.D., Izaurralde, E., Hanover, J.A., Conti, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.297 
• R-Value Work: 0.259 
• R-Value Observed: 0.259 

Literature

The Superhelical Tpr-Repeat Domain of O-Linked Glcnac Transferase Exhibits Structural Similarities to Importin Alpha

Jinek, M., Rehwinkel, J., Lazarus, B.D., Izaurralde, E., Hanover, J.A., Conti, E.

(2004) Nat Struct Mol Biol 11: 1001

• PubMed: 15361863 
• DOI: 10.1038/nsmb833
• Primary Citation of Related Structures:  
  1W3B


• PubMed Abstract: 
  

Addition of N-acetylglucosamine (GlcNAc) is a ubiquitous form of intracellular glycosylation catalyzed by the conserved O-linked GlcNAc transferase (OGT). OGT contains an N-terminal domain of tetratricopeptide (TPR) repeats that mediates the recognition of a broad range of target proteins. Components of the nuclear pore complex are major OGT targets, as OGT depletion by RNA interference (RNAi) results in the loss of GlcNAc modification at the nuclear envelope. To gain insight into the mechanism of target recognition, we solved the crystal structure of the homodimeric TPR domain of human OGT, which contains 11.5 TPR repeats. The repeats form an elongated superhelix. The concave surface of the superhelix is lined by absolutely conserved asparagines, in a manner reminiscent of the peptide-binding site of importin alpha. Based on this structural similarity, we propose that OGT uses an analogous molecular mechanism to recognize its targets.

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Organizational Affiliation: 

Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYLTRANSFERASE 110	A, B	388	Homo sapiens	Mutation(s): 0  Gene Names: OGT EC: 2.4.1 (PDB Primary Data), 2.4.1.255 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O15294 (Homo sapiens) Explore O15294  Go to UniProtKB:  O15294
PHAROS:  O15294 GTEx:  ENSG00000147162

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.297 
• R-Value Work: 0.259 
• R-Value Observed: 0.259 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.32	α = 105.08
b = 75.51	β = 105.14
c = 77.67	γ = 110.28

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XDS	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-14 
• Released Date: 2004-09-09 
Deposition Author(s): Jinek, M., Rehwinkel, J., Lazarus, B.D., Izaurralde, E., Hanover, J.A., Conti, E.

Revision History  

• Version 1.0: 2004-09-09
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance