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 generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 152.51 kDa 
• Atom Count: 11843 
• Modelled Residue Count: 1370 
• Deposited 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)
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.199 
• R-Value Work: 0.167 
• R-Value Observed: 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:  
  2CH5, 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAGK PROTEIN	A, B, C, D	347	Homo sapiens	Mutation(s): 0  Gene Names: NAGK EC: 2.7.1.59
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJ70 (Homo sapiens) Explore Q9UJ70  Go to UniProtKB:  Q9UJ70
PHAROS:  Q9UJ70 GTEx:  ENSG00000124357

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDG (Subject of Investigation/LOI)	K [auth D]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	F [auth A], H [auth B], J [auth C], L [auth D], M [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.199 
• R-Value Work: 0.167 
• R-Value Observed: 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
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Ligand Structure Quality Assessment  

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
  Changes: Advisory, Refinement description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary