Biological Assembly 1  

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Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 320583.69 
• Atom Count: 22381 
• Residue Count: 2802 
• Unique protein chains: 1

3KHU

Crystal structure of human UDP-glucose dehydrogenase Glu161Gln, in complex with thiohemiacetal intermediate

• DOI: 10.2210/pdb3KHU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2009-10-30 Released: 2009-11-17 
• Deposition Author(s): Chaikuad, A., Egger, S., Yue, W.W., Guo, K., Sethi, R., Filippakopoulos, P., Muniz, J.R.C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A.M., Kavanagh, K.L., Nidetzky, B., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.225 
• R-Value Work: 0.195 

Literature

Structural and Kinetic Evidence That Catalytic Reaction of Human UDP-glucose 6-Dehydrogenase Involves Covalent Thiohemiacetal and Thioester Enzyme Intermediates.

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

(2012) J.Biol.Chem. 287: 2119-2129

• PubMed: 22123821 
• DOI: 10.1074/jbc.M111.313015


• PubMed Abstract: 
  

Biosynthesis of UDP-glucuronic acid by UDP-glucose 6-dehydrogenase (UGDH) occurs through the four-electron oxidation of the UDP-glucose C6 primary alcohol in two NAD(+)-dependent steps. The catalytic reaction of UGDH is thought to involve a Cys nucleophile that promotes formation of a thiohemiacetal enzyme intermediate in the course of the first oxidation step. The thiohemiacetal undergoes further oxidation into a thioester, and hydrolysis of the thioester completes the catalytic cycle. Herein we present crystallographic and kinetic evidence for the human form of UGDH that clarifies participation of covalent catalysis in the enzymatic mechanism. Substitution of the putative catalytic base for water attack on the thioester (Glu(161)) by an incompetent analog (Gln(161)) gave a UGDH variant (E161Q) in which the hydrolysis step had become completely rate-limiting so that a thioester enzyme intermediate accumulated at steady state. By crystallizing E161Q in the presence of 5 mm UDP-glucose and 2 mm NAD(+), we succeeded in trapping a thiohemiacetal enzyme intermediate and determined its structure at 2.3 Å resolution. Cys(276) was covalently modified in the structure, establishing its role as catalytic nucleophile of the reaction. The thiohemiacetal reactive C6 was in a position suitable to become further oxidized by hydride transfer to NAD(+). The proposed catalytic mechanism of human UGDH involves Lys(220) as general base for UDP-glucose alcohol oxidation and for oxyanion stabilization during formation and breakdown of the thiohemiacetal and thioester enzyme intermediates. Water coordinated to Asp(280) deprotonates Cys(276) to function as an aldehyde trap and also provides oxyanion stabilization. Glu(161) is the Brønsted base catalytically promoting the thioester hydrolysis.

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Organizational Affiliation: 

Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, A-8010 Graz, Austria.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
UDP-glucose 6-dehydrogenase	A, B, C, D, E, F	467	Homo sapiens	Mutation(s): 1  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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EPE	D	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HEPES C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
UPG	A, B, C, D, E, F	URIDINE-5'-DIPHOSPHATE-GLUCOSE URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER C15 H24 N2 O17 P2 HSCJRCZFDFQWRP-JZMIEXBBSA-N
EDO	A, B, C, E	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.225 
• R-Value Work: 0.195 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 203.540	α = 90.00
b = 207.340	β = 90.00
c = 93.400	γ = 90.00

Software Package:

Software Name	Purpose
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-10-30 
• Released Date: 2009-11-17 
• Deposition Author(s): Chaikuad, A., Egger, S., Yue, W.W., Guo, K., Sethi, R., Filippakopoulos, P., Muniz, J.R.C., von Delft, F., Bountra, C., Arrowsmith, C.H., Weigelt, J., Edwards, A.M., Kavanagh, K.L., Nidetzky, B., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History 

• Version 1.0: 2009-11-17
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Version format compliance
• Version 1.2: 2011-12-07
  Type: Database references
• Version 1.3: 2012-01-11
  Type: Database references
• Version 1.4: 2012-02-01
  Type: Database references