4ZHT

Crystal structure of UDP-GlcNAc 2-epimerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanism and inhibition of human UDP-GlcNAc 2-epimerase, the key enzyme in sialic acid biosynthesis.

Chen, S.C.Huang, C.H.Lai, S.J.Yang, C.S.Hsiao, T.H.Lin, C.H.Fu, P.K.Ko, T.P.Chen, Y.

(2016) Sci Rep 6: 23274-23274

  • DOI: 10.1038/srep23274
  • Primary Citation of Related Structures:  
    4ZHT

  • PubMed Abstract: 
  • The bifunctional enzyme UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE) plays a key role in sialic acid production. It is different from the non-hydrolyzing enzymes for bacterial cell wall biosynthesis, and it is feed-back inhibited by the downstream product ...

    The bifunctional enzyme UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE) plays a key role in sialic acid production. It is different from the non-hydrolyzing enzymes for bacterial cell wall biosynthesis, and it is feed-back inhibited by the downstream product CMP-Neu5Ac. Here the complex crystal structure of the N-terminal epimerase part of human GNE shows a tetramer in which UDP binds to the active site and CMP-Neu5Ac binds to the dimer-dimer interface. The enzyme is locked in a tightly closed conformation. By comparing the UDP-binding modes of the non-hydrolyzing and hydrolyzing UDP-GlcNAc epimerases, we propose a possible explanation for the mechanistic difference. While the epimerization reactions of both enzymes are similar, Arg113 and Ser302 of GNE are likely involved in product hydrolysis. On the other hand, the CMP-Neu5Ac binding mode clearly elucidates why mutations in Arg263 and Arg266 can cause sialuria. Moreover, full-length modelling suggests a channel for ManNAc trafficking within the bifunctional enzyme.


    Organizational Affiliation

    Department of Biotechnology, Hungkuang University, Taichung, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase ABCD411Homo sapiensMutation(s): 0 
Gene Names: GNEGLCNE
EC: 3.2.1.183 (PDB Primary Data), 2.7.1.60 (UniProt)
Find proteins for Q9Y223 (Homo sapiens)
Explore Q9Y223 
Go to UniProtKB:  Q9Y223
NIH Common Fund Data Resources
PHAROS:  Q9Y223
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NCC
Query on NCC

Download Ideal Coordinates CCD File 
A, B, C, D
CYTIDINE-5'-MONOPHOSPHATE-5-N-ACETYLNEURAMINIC ACID
C20 H31 N4 O16 P
TXCIAUNLDRJGJZ-BILDWYJOSA-N
 Ligand Interaction
UDP
Query on UDP

Download Ideal Coordinates CCD File 
A, B, C, D
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
 Ligand Interaction
BM7
Query on BM7

Download Ideal Coordinates CCD File 
C
2-acetamido-2-deoxy-beta-D-mannopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-OZRXBMAMSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,C,DL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.041α = 90
b = 98.102β = 96.05
c = 154.722γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2016-11-09
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary