Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 152505.41 
• Atom Count: 10571 
• Residue Count: 1388 
• Unique protein chains: 1

2CH5

Crystal structure of human N-acetylglucosamine kinase in complex with N-acetylglucosamine

• DOI: 10.2210/pdb2CH5/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2006-03-13 Released: 2006-09-18 
• Deposition Author(s): Weihofen, W.A., Berger, M., Chen, H., Saenger, W., Hinderlich, S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.199 
• R-Value Work: 0.167 

Literature

Structures of Human N-Acetylglucosamine Kinase in Two Complexes with N-Acetylglucosamine and with Adp/Glucose: Insights Into Substrate Specificity and Regulation.

Weihofen, W.A., Berger, M., Chen, H., Saenger, W., Hinderlich, S.

(2006) J.Mol.Biol. 364: 388

• PubMed: 17010375 
• DOI: 10.1016/j.jmb.2006.08.085
• Primary Citation of Related Structures:  
  2CH6


• PubMed Abstract: 
  

N-Acetylglucosamine (GlcNAc), a major component of complex carbohydrates, is synthesized de novo or salvaged from lysosomally degraded glycoconjugates and from nutritional sources. The salvage pathway requires that GlcNAc kinase converts GlcNAc to GlcNAc-6-phosphate, a component utilized in UDP-GlcNAc biosynthesis or energy metabolism. GlcNAc kinase belongs to the sugar kinase/Hsp70/actin superfamily that catalyze phosphoryl transfer from ATP to their respective substrates, and in most cases catalysis is associated with a large conformational change in which the N-terminal small and C-terminal large domains enclose the substrates. Here we report two crystal structures of homodimeric human GlcNAc kinase, one in complex with GlcNAc and the other in complex with ADP and glucose. The active site of GlcNAc kinase is located in a deep cleft between the two domains of the V-shaped monomer. The enzyme adopts a "closed" configuration in the GlcNAc-bound complex and GlcNAc interacts with residues of both domains. In addition, the N-acetyl methyl group contacts residues of the other monomer in the homodimer, a unique feature compared to other members of the sugar kinase/Hsp70/actin superfamily. This contrasts an "open" configuration in the ADP/glucose-bound structure, where glucose cannot form these interactions, explaining its low binding affinity for GlcNAc kinase. Our results support functional implications derived from apo crystal structures of GlcNAc kinases from Chromobacter violaceum and Porphyromonas gingivalis and show that Tyr205, which is phosphorylated in thrombin-activated platelets, lines the GlcNAc binding pocket. This suggests that phosphorylation of Tyr205 may modulate GlcNAc kinase activity and/or specificity.

---

Organizational Affiliation: 

Freie Universität Berlin, Institut für Chemie und Biochemie-Kristallographie, Takustrasse 6, 14195 Berlin-Dahlem, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NAGK PROTEIN	A, B, C, D	347	Homo sapiens	Mutation(s): 0  Gene Names: NAGK EC: 2.7.1.59
Find proteins for Q9UJ70 (Homo sapiens) Go to Gene View: NAGK Go to UniProtKB:  Q9UJ70

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A, B, C, D	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NDG	D	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG	A, B, C	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.199 
• R-Value Work: 0.167 
• Space Group: P 1

Unit Cell:

Length (Å)	Angle (°)
a = 57.537	α = 63.43
b = 98.482	β = 75.66
c = 101.981	γ = 75.06

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
SCALEPACK	data scaling
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-03-13 
• Released Date: 2006-09-18 
• Deposition Author(s): Weihofen, W.A., Berger, M., Chen, H., Saenger, W., Hinderlich, S.

Revision History 

• Version 1.0: 2006-09-18
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Refinement description, Version format compliance