2QG4

Crystal structure of human UDP-glucose dehydrogenase product complex with UDP-glucuronate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure and mechanism of human UDP-glucose 6-dehydrogenase.

Egger, S.Chaikuad, A.Kavanagh, K.L.Oppermann, U.Nidetzky, B.

(2011) J.Biol.Chem. 286: 23877-23887

  • DOI: 10.1074/jbc.M111.234682
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Elevated production of the matrix glycosaminoglycan hyaluronan is strongly implicated in epithelial tumor progression. Inhibition of synthesis of the hyaluronan precursor UDP-glucuronic acid (UDP-GlcUA) therefore presents an emerging target for cance ...

    Elevated production of the matrix glycosaminoglycan hyaluronan is strongly implicated in epithelial tumor progression. Inhibition of synthesis of the hyaluronan precursor UDP-glucuronic acid (UDP-GlcUA) therefore presents an emerging target for cancer therapy. Human UDP-glucose 6-dehydrogenase (hUGDH) catalyzes, in two NAD(+)-dependent steps without release of intermediate aldehyde, the biosynthetic oxidation of UDP-glucose (UDP-Glc) to UDP-GlcUA. Here, we present a structural characterization of the hUGDH reaction coordinate using crystal structures of the apoenzyme and ternary complexes of the enzyme bound with UDP-Glc/NADH and UDP-GlcUA/NAD(+). The quaternary structure of hUGDH is a disc-shaped trimer of homodimers whose subunits consist of two discrete α/β domains with the active site located in the interdomain cleft. Ternary complex formation is accompanied by rigid-body and restrained movement of the N-terminal NAD(+) binding domain, sequestering substrate and coenzyme in their reactive positions through interdomain closure. By alternating between conformations in and out of the active site during domain motion, Tyr(14), Glu(161), and Glu(165) participate in control of coenzyme binding and release during 2-fold oxidation. The proposed mechanism of hUGDH involves formation and breakdown of thiohemiacetal and thioester intermediates whereby Cys(276) functions as the catalytic nucleophile. Stopped-flow kinetic data capture the essential deprotonation of Cys(276) in the course of the first oxidation step, allowing the thiolate side chain to act as a trap of the incipient aldehyde. Because thiohemiacetal intermediate accumulates at steady state under physiological reaction conditions, hUGDH inhibition might best explore ligand binding to the NAD(+) binding domain.


    Organizational Affiliation

    Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/1, A-8010 Graz, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-glucose 6-dehydrogenase
A, B, C, D, E, F, G, H
467Homo sapiensMutation(s): 0 
Gene Names: UGDH
EC: 1.1.1.22
Find proteins for O60701 (Homo sapiens)
Go to Gene View: UGDH
Go to UniProtKB:  O60701
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UGA
Query on UGA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID
UDP-GLUCURONIC ACID
C15 H22 N2 O18 P2
HDYANYHVCAPMJV-LXQIFKJMSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
B, D, F, H
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
B, C, F, G
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.176 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 193.868α = 90.00
b = 193.868β = 90.00
c = 352.223γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2007-07-10
    Type: Initial release
  • Version 1.1: 2008-05-05
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Refinement description, Version format compliance
  • Version 1.3: 2011-08-31
    Type: Database references
  • Version 1.4: 2017-10-18
    Type: Refinement description