5TJH

hUGDH A136M Substitution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

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This is version 1.4 of the entry. See complete history


Literature

Allostery and Hysteresis Are Coupled in Human UDP-Glucose Dehydrogenase.

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

(2017) Biochemistry 56: 202-211

  • DOI: 10.1021/acs.biochem.6b01044
  • Primary Citation of Related Structures:  
    5TJH

  • PubMed Abstract: 
  • Human UDP-glucose dehydrogenase (hUGDH) is regulated by an atypical allosteric mechanism in which the feedback inhibitor UDP-xylose (UDP-Xyl) competes with the substrate for the active site. Binding of UDP-Xyl triggers the T131-loop/α6 allosteric switch, which converts the hexameric structure of hUGDH into an inactive, horseshoe-shaped complex (E Ω ) ...

    Human UDP-glucose dehydrogenase (hUGDH) is regulated by an atypical allosteric mechanism in which the feedback inhibitor UDP-xylose (UDP-Xyl) competes with the substrate for the active site. Binding of UDP-Xyl triggers the T131-loop/α6 allosteric switch, which converts the hexameric structure of hUGDH into an inactive, horseshoe-shaped complex (E Ω ). This allosteric transition buries residue A136 in the protein core to produce a subunit interface that favors the E Ω structure. Here we use a methionine substitution to prevent the burial of A136 and trap the T131-loop/α6 switch in the active conformation. We show that hUGDH A136M does not exhibit substrate cooperativity, which is strong evidence that the methionine substitution prevents the formation of the low-UDP-Glc-affinity E Ω state. In addition, the inhibitor affinity of hUGDH A136M is reduced 14-fold, which most likely represents the K i for competitive inhibition in the absence of the allosteric transition to the higher-affinity E Ω state. hUGDH also displays a lag in progress curves, which is caused by a slow, substrate-induced isomerization that activates the enzyme. Stopped-flow analysis shows that hUGDH A136M does not exhibit hysteresis, which suggests that the T131-loop/α6 switch is the source of the slow isomerization. This interpretation is supported by the 2.05 Å resolution crystal structure of hUGDH A136M , which shows that the A136M substitution has stabilized the active conformation of the T131-loop/α6 allosteric switch. This work shows that the T131-loop/α6 allosteric switch couples allostery and hysteresis in hUGDH.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
UDP-glucose 6-dehydrogenaseA, B, C, D, E, F494Homo sapiensMutation(s): 1 
Gene Names: UGDH
EC: 1.1.1.22
UniProt & NIH Common Fund Data Resources
Find proteins for O60701 (Homo sapiens)
Explore O60701 
Go to UniProtKB:  O60701
PHAROS:  O60701
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.35α = 64.82
b = 104.59β = 68.35
c = 107.71γ = 73.72
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
PHASERphasing

Structure Validation

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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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-02
    Type: Initial release
  • Version 1.1: 2017-01-04
    Changes: Database references
  • Version 1.2: 2017-01-25
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Refinement description
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence