Ligand bound full length hUGDH with A104L substitution

Experimental Data Snapshot

  • Resolution: 2.53 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Hysteresis and Allostery in Human UDP-Glucose Dehydrogenase Require a Flexible Protein Core.

Beattie, N.R.Pioso, B.J.Sidlo, A.M.Keul, N.D.Wood, Z.A.

(2018) Biochemistry 57: 6848-6859

  • DOI: https://doi.org/10.1021/acs.biochem.8b00497
  • Primary Citation of Related Structures:  
    6C4J, 6C4K

  • PubMed Abstract: 

    Human UDP-glucose dehydrogenase (hUGDH) oxidizes UDP-glucose to UDP-glucuronic acid, an essential substrate in the phase II metabolism of drugs. The activity of hUGDH is regulated by the conformation of a buried allosteric switch (T131 loop/α6 helix). Substrate binding induces the allosteric switch to slowly isomerize from an inactive E* conformation to the active E state, which can be observed as enzyme hysteresis. When the feedback inhibitor UDP-xylose binds, the allosteric switch and surrounding residues in the protein core repack, converting the hexamer into an inactive, horseshoe-shaped complex (E Ω ). This allosteric transition is facilitated by large cavities and declivities in the protein core that provide the space required to accommodate the alternate packing arrangements. Here, we have used the A104L substitution to fill a cavity in the E state and sterically prevent repacking of the core into the E Ω state. Steady state analysis shows that hUGDH A104L binds UDP-xylose with lower affinity and that the inhibition is no longer cooperative. This means that the allosteric transition to the high-UDP-xylose affinity E Ω state is blocked by the substitution. The crystal structures of hUGDH A104L show that the allosteric switch still adopts the E and E* states, albeit with a more rigid protein core. However, the progress curves of hUGDH A104L do not show hysteresis, which suggests that the E* and E states are now in rapid equilibrium. Our data suggest that hysteresis in native hUGDH originates from the conformational entropy of the E* state protein core.

  • Organizational Affiliation

    Department of Biochemistry & Molecular Biology , University of Georgia , Athens , Georgia 30602 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UDP-glucose 6-dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
494Homo sapiensMutation(s): 1 
Gene Names: UGDH
UniProt & NIH Common Fund Data Resources
Find proteins for O60701 (Homo sapiens)
Explore O60701 
Go to UniProtKB:  O60701
PHAROS:  O60701
GTEx:  ENSG00000109814 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60701
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
AB [auth K]
CA [auth E]
GA [auth F]
GB [auth L]
LA [auth G]
AB [auth K],
CA [auth E],
GA [auth F],
GB [auth L],
LA [auth G],
M [auth A],
P [auth B],
QA [auth H],
T [auth C],
TA [auth I],
W [auth D],
XA [auth J]
C21 H27 N7 O14 P2
Query on UPG

Download Ideal Coordinates CCD File 
BB [auth K]
DA [auth E]
HA [auth F]
HB [auth L]
MA [auth G]
BB [auth K],
DA [auth E],
HA [auth F],
HB [auth L],
MA [auth G],
N [auth A],
Q [auth B],
RA [auth H],
U [auth C],
UA [auth I],
X [auth D],
YA [auth J]
C15 H24 N2 O17 P2
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
EA [auth E]
EB [auth K]
IA [auth F]
JA [auth F]
AA [auth D],
EA [auth E],
EB [auth K],
IA [auth F],
JA [auth F],
OA [auth G],
V [auth C],
Z [auth D]
O4 S
Query on PGO

Download Ideal Coordinates CCD File 
BA [auth D]
FA [auth E]
FB [auth K]
KA [auth F]
KB [auth L]
BA [auth D],
FA [auth E],
FB [auth K],
KA [auth F],
KB [auth L],
PA [auth G]
C3 H8 O2
Query on CL

Download Ideal Coordinates CCD File 
CB [auth K]
DB [auth K]
IB [auth L]
JB [auth L]
NA [auth G]
CB [auth K],
DB [auth K],
IB [auth L],
JB [auth L],
NA [auth G],
O [auth A],
R [auth B],
S [auth B],
SA [auth H],
VA [auth I],
WA [auth I],
Y [auth D],
ZA [auth J]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.53 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 403.55α = 90
b = 112.59β = 98.5
c = 184.67γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
Cootmodel building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM114298

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-12-05
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references