Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 117.59 kDa 
• Atom Count: 7140 
• Modelled Residue Count: 861 
• Deposited Residue Count: 1022 
• Unique protein chains: 2

5VVU

Structural Investigations of the Substrate Specificity of Human O-GlcNAcase

• PDB DOI: 10.2210/pdb5VVU/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-20 Released: 2017-09-27 
• Deposition Author(s): Li, B., Jiang, J., Li, H., Hu, C.-W.
• Funding Organization(s): University of Wisconsin-Madison

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.275 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

Literature

Structural insights into the substrate binding adaptability and specificity of human O-GlcNAcase.

Li, B., Li, H., Hu, C.W., Jiang, J.

(2017) Nat Commun 8: 666-666

• PubMed: 28939839 
• DOI: 10.1038/s41467-017-00865-1
• Primary Citation of Related Structures:  
  5VVO, 5VVT, 5VVU, 5VVV, 5VVX


• PubMed Abstract: 
  

The O-linked β-N-acetyl glucosamine (O-GlcNAc) modification dynamically regulates the functions of numerous proteins. A single human enzyme O-linked β-N-acetyl glucosaminase (O-GlcNAcase or OGA) hydrolyzes this modification. To date, it remains largely unknown how OGA recognizes various substrates. Here we report the structures of OGA in complex with each of four distinct glycopeptide substrates that contain a single O-GlcNAc modification on a serine or threonine residue. Intriguingly, these glycopeptides bind in a bidirectional yet conserved conformation within the substrate-binding cleft of OGA. This study provides fundamental insights into a general principle that confers the substrate binding adaptability and specificity to OGA in O-GlcNAc regulation.O-linked β-N-acetyl glucosamine (O-GlcNAc) is an important protein modification that is hydrolyzed by O-GlcNAcase (OGA). Here the authors give insights into OGA substrate recognition by presenting four human OGA structures complexed with glycopeptide substrates containing a single O-GlcNAc modification on either a serine or threonine.

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Organizational Affiliation: 

Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein O-GlcNAcase	A, C	504	Homo sapiens	Mutation(s): 0  Gene Names: MGEA5, HEXC, KIAA0679, MEA5 EC: 3.2.1.169 (PDB Primary Data), 3.2.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for O60502 (Homo sapiens) Explore O60502  Go to UniProtKB:  O60502
PHAROS:  O60502 GTEx:  ENSG00000198408

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TAB1 peptide	B, D	7	Homo sapiens	Mutation(s): 0  Gene Names: TAB1, MAP3K7IP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15750 (Homo sapiens) Explore Q15750  Go to UniProtKB:  Q15750
PHAROS:  Q15750 GTEx:  ENSG00000100324

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth B], F [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.275 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.507	α = 90
b = 96.06	β = 114.51
c = 88.968	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-05-20 
• Released Date: 2017-09-27 
Deposition Author(s): Li, B., Jiang, J., Li, H., Hu, C.-W.

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Funding Organization	Location	Grant Number
University of Wisconsin-Madison	United States	--

Revision History  

• Version 1.0: 2017-09-27
  Type: Initial release
  
• Version 1.1: 2017-10-04
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary