Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | 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 PISA (software)

Macromolecule Content

• Total Structure Weight: 17.32 kDa 
• Atom Count: 1388 
• Modelled Residue Count: 147 
• Deposited Residue Count: 149 
• Unique protein chains: 1

3T90

Crystal structure of glucosamine-6-phosphate N-acetyltransferase from Arabidopsis thaliana

• PDB DOI: 10.2210/pdb3T90/pdb

• Classification: TRANSFERASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-02 Released: 2012-04-11 
• Deposition Author(s): Grishkovskaya, I., Herter, T., Riegler, H., Usadel, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.201 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Literature

Crystal structure and functional characterization of a glucosamine-6-phosphate N-acetyltransferase from Arabidopsis thaliana.

Riegler, H., Herter, T., Grishkovskaya, I., Lude, A., Ryngajllo, M., Bolger, M.E., Essigmann, B., Usadel, B.

(2012) Biochem J 443: 427-437

• PubMed: 22329777 
• DOI: 10.1042/BJ20112071
• Primary Citation of Related Structures:  
  3T90


• PubMed Abstract: 
  

GlcNAc (N-acetylglucosamine) is an essential part of the glycan chain in N-linked glycoproteins. It is a building block for polysaccharides such as chitin, and several glucosaminoglycans and proteins can be O-GlcNAcylated. The deacetylated form, glucosamine, is an integral part of GPI (glycosylphosphatidylinositol) anchors. Both are incorporated into polymers by glycosyltransferases that utilize UDP-GlcNAc. This UDP-sugar is synthesized in a short pathway comprising four steps starting from fructose 6-phosphate. GNA (glucosamine-6-phosphate N-acetyltransferase) catalyses the second of these four reactions in the de novo synthesis in eukaryotes. A phylogenetic analysis revealed that only one GNA isoform can be found in most of the species investigated and that the most likely Arabidopsis candidate is encoded by the gene At5g15770 (AtGNA). qPCR (quantitative PCR) revealed the ubiquitous expression of AtGNA in all organs of Arabidopsis plants. Heterologous expression of AtGNA showed that it is highly active between pH 7 and 8 and at temperatures of 30-40°C. It showed Km values of 231 μM for glucosamine 6-phosphate and 33 μM for acetyl-CoA respectively and a catalytic efficiency comparable with that of other GNAs characterized. The solved crystal structure of AtGNA at a resolution of 1.5 Å (1 Å=0.1 nm) revealed a very high structural similarity to crystallized GNA proteins from Homo sapiens and Saccharomyces cerevisiae despite less well conserved protein sequence identity.

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Organizational Affiliation: 

Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-6-phosphate acetyltransferase 1	A	149	Arabidopsis thaliana	Mutation(s): 0  Gene Names: F14F8_150, GNA1, At5g15770, F14F8.150 EC: 2.3.1.4
UniProt
Find proteins for Q9LFU9 (Arabidopsis thaliana) Explore Q9LFU9  Go to UniProtKB:  Q9LFU9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	B [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.201 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.52	α = 90
b = 47.174	β = 100.74
c = 42.223	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-08-02 
• Released Date: 2012-04-11 
Deposition Author(s): Grishkovskaya, I., Herter, T., Riegler, H., Usadel, B.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release