Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 115.41 kDa 
• Atom Count: 8731 
• Residue Count: 975 
• Unique protein chains: 1

1JV1

CRYSTAL STRUCTURE OF HUMAN AGX1 COMPLEXED WITH UDPGLCNAC

• DOI: 10.2210/pdb1JV1/pdb

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


• Deposited: 2001-08-28 Released: 2002-08-28 
• Deposition Author(s): Peneff, C., Bourne, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.220 
• R-Value Work: 0.183 

Literature

Crystal structures of two human pyrophosphorylase isoforms in complexes with UDPGlc(Gal)NAc: role of the alternatively spliced insert in the enzyme oligomeric assembly and active site architecture.

Peneff, C., Ferrari, P., Charrier, V., Taburet, Y., Monnier, C., Zamboni, V., Winter, J., Harnois, M., Fassy, F., Bourne, Y.

(2001) EMBO J 20: 6191-6202

• PubMed: 11707391 
• DOI: 10.1093/emboj/20.22.6191
• Primary Citation of Related Structures:  
  1JV3, 1JV1, 1JVD, 1JVG


• PubMed Abstract: 
  

The recently published human genome with its relatively modest number of genes has highlighted the importance of post-transcriptional and post-translational modifications, such as alternative splicing or glycosylation, in generating the complexities of human biology. The human UDP-N-acetylglucosamine (UDPGlcNAc) pyrophosphorylases AGX1 and AGX2, which differ in sequence by an alternatively spliced 17 residue peptide, are key enzymes synthesizing UDPGlcNAc, an essential precursor for protein glycosylation. To better understand the catalytic mechanism of these enzymes and the role of the alternatively spliced segment, we have solved the crystal structures of AGX1 and AGX2 in complexes with UDPGlcNAc (at 1.9 and 2.4 A resolution, respectively) and UDPGalNAc (at 2.2 and 2.3 A resolution, respectively). Comparison with known structures classifies AGX1 and AGX2 as two new members of the SpsA-GnT I Core superfamily and, together with mutagenesis analysis, helps identify residues critical for catalysis. Most importantly, our combined structural and biochemical data provide evidence for a change in the oligomeric assembly accompanied by a significant modification of the active site architecture, a result suggesting that the two isoforms generated by alternative splicing may have distinct catalytic properties.

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Organizational Affiliation: 

AFMB, UMR 6098 CNRS, 31 chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GlcNAc1P uridyltransferase isoform 1: AGX1	A, B	505	Homo sapiens	Mutation(s): 0  Gene Names: UAP1, SPAG2 EC: 2.7.7 (PDB Primary Data), 2.7.7.83 (UniProt), 2.7.7.23 (UniProt)
Find proteins for Q16222 (Homo sapiens) Explore Q16222  Go to UniProtKB:  Q16222
NIH Common Fund Data Resources
PHAROS:  Q16222 GTEx:  ENSG00000117143

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UD1	A, B	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE C17 H27 N3 O17 P2 LFTYTUAZOPRMMI-CFRASDGPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.220 
• R-Value Work: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.829	α = 90
b = 70.904	β = 95.25
c = 96.18	γ = 90

Software Package:

Software Name	Purpose
SnB	phasing
CNS	refinement
DENZO	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-08-28 
• Released Date: 2002-08-28 
Deposition Author(s): Peneff, C., Bourne, Y.

Revision History 

• Version 1.0: 2002-08-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description