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: 38.00 kDa 
• Atom Count: 2802 
• Residue Count: 309 
• Unique protein chains: 1

2YHW

High-resolution crystal structures of N-Acetylmannosamine kinase: Insights about substrate specificity, activity and inhibitor modelling.

• DOI: 10.2210/pdb2YHW/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-05-08 Released: 2012-02-29 
• Deposition Author(s): Martinez, J., Nguyen, L.D., Tauberger, E., Hinderlich, S., Zimmer, R., Tauberger, E., Reutter, W., Saenger, W., Fan, H., Moniot, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.170 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 

Literature

Crystal Structures of N-Acetylmannosamine Kinase Provide Insights Into Enzyme Specificity and Inhibition

Martinez, J., Nguyen, L.D., Tauberger, E., Hinderlich, S., Reutter, W., Fan, H., Saenger, W., Moniot, S.

(2012) J Biol Chem 287: 13656

• PubMed: 22343627 
• DOI: 10.1074/jbc.M111.318170
• Primary Citation of Related Structures:  
  2YHY, 2YHW, 2YI1


• PubMed Abstract: 
  

Sialic acids are essential components of membrane glycoconjugates. They are responsible for the interaction, structure, and functionality of all deuterostome cells and have major functions in cellular processes in health and diseases. The key enzyme of the biosynthesis of sialic acid is the bifunctional UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase that transforms UDP-N-acetylglucosamine to N-acetylmannosamine (ManNAc) followed by its phosphorylation to ManNAc 6-phosphate and has a direct impact on the sialylation of cell surface components. Here, we present the crystal structures of the human N-acetylmannosamine kinase (MNK) domain of UDP-N-acetylglucosamine-2-epimerase/N-acetylmannosamine kinase in complexes with ManNAc at 1.64 Å resolution, MNK·ManNAc·ADP (1.82 Å) and MNK·ManNAc 6-phosphate · ADP (2.10 Å). Our findings offer detailed insights in the active center of MNK and serve as a structural basis to design inhibitors. We synthesized a novel inhibitor, 6-O-acetyl-ManNAc, which is more potent than those previously tested. Specific inhibitors of sialic acid biosynthesis may serve to further study biological functions of sialic acid.

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Organizational Affiliation: 

From the Institut für Chemie und Biochemie-Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BIFUNCTIONAL UDP-N-ACETYLGLUCOSAMINE 2-EPIMERASE/N-ACETYLMANNOSAMINE KINASE	A	343	Homo sapiens	Mutation(s): 0  Gene Names: GNE, GLCNE EC: 2.7.1.60 (PDB Primary Data), 3.2.1.183 (UniProt)
Find proteins for Q9Y223 (Homo sapiens) Explore Q9Y223  Go to UniProtKB:  Q9Y223
NIH Common Fund Data Resources
PHAROS:  Q9Y223 GTEx:  ENSG00000159921

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PE	A	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
BM3	A	2-acetamido-2-deoxy-alpha-D-mannopyranose C8 H15 N O6 OVRNDRQMDRJTHS-UOLFYFMNSA-N
PGE	A	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNN	A	L-PEPTIDE LINKING	C4 H6 N2 O2		ASN

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
BM3	Kd :  2500   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.170 
• R-Value Work: 0.148 
• R-Value Observed: 0.149 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.73	α = 90
b = 90.73	β = 90
c = 100.78	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-05-08 
• Released Date: 2012-02-29 
Deposition Author(s): Martinez, J., Nguyen, L.D., Tauberger, E., Hinderlich, S., Zimmer, R., Tauberger, E., Reutter, W., Saenger, W., Fan, H., Moniot, S.

Revision History 

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2012-05-02
  Changes: Other
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary