4Z0G

Structure of the IMPDH from Ashbya gossypii bound to GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases.

Buey, R.M.Ledesma-Amaro, R.Velazquez-Campoy, A.Balsera, M.Chagoyen, M.de Pereda, J.M.Revuelta, J.L.

(2015) Nat Commun 6: 8923-8923

  • DOI: https://doi.org/10.1038/ncomms9923
  • Primary Citation of Related Structures:  
    4Z0G, 4Z87

  • PubMed Abstract: 

    Inosine-5'-monophosphate dehydrogenase (IMPDH) plays key roles in purine nucleotide metabolism and cell proliferation. Although IMPDH is a widely studied therapeutic target, there is limited information about its physiological regulation. Using Ashbya gossypii as a model, we describe the molecular mechanism and the structural basis for the allosteric regulation of IMPDH by guanine nucleotides. We report that GTP and GDP bind to the regulatory Bateman domain, inducing octamers with compromised catalytic activity. Our data suggest that eukaryotic and prokaryotic IMPDHs might have developed different regulatory mechanisms, with GTP/GDP inhibiting only eukaryotic IMPDHs. Interestingly, mutations associated with human retinopathies map into the guanine nucleotide-binding sites including a previously undescribed non-canonical site and disrupt allosteric inhibition. Together, our results shed light on the mechanisms of the allosteric regulation of enzymes mediated by Bateman domains and provide a molecular basis for certain retinopathies, opening the door to new therapeutic approaches.


  • Organizational Affiliation

    Metabolic Engineering Group, Dpto. Microbiología y Genética. Universidad de Salamanca, Campus Miguel de Unamuno, Edificio Departamental, Salamanca 37007, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
A, B
413Eremothecium gossypii ATCC 10895Mutation(s): 0 
Gene Names: AGOS_AER117W
EC: 1.1.1.205
UniProt
Find proteins for Q756Z6 (Eremothecium gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056))
Explore Q756Z6 
Go to UniProtKB:  Q756Z6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ756Z6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5GP
Query on 5GP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 
  • Space Group: P 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.48α = 90
b = 117.48β = 90
c = 56.525γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release
  • Version 2.0: 2024-01-10
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description