4Z0G | pdb_00004z0g

Structure of the IMPDH from Ashbya gossypii bound to GMP

• PDB DOI: https://doi.org/10.2210/pdb4Z0G/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Eremothecium gossypii ATCC 10895
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-26 Released: 2015-11-25 
• Deposition Author(s): Buey, R.M., de Pereda, J.M., Revuelta, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.148 (Depositor), 0.152 (DCC) 
• R-Value Work: 
  0.124 (Depositor), 0.131 (DCC) 
• R-Value Observed: 
  0.125 (Depositor) 

Starting Model: experimental

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

• PubMed: 26558346 
• DOI: https://doi.org/10.1038/ncomms9923
• Primary Citation 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.

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Organizational Affiliation: 
• Metabolic Engineering Group, Dpto. Microbiología y Genética. Universidad de Salamanca, Campus Miguel de Unamuno, Edificio Departamental, Salamanca 37007, Spain.
Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, C/Mariano Esquillor, Zaragoza 50018, Spain.
Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza 50009, Spain.
Instituto de Investigaciones Sanitarias de Aragón (IIS-A), Zaragoza 50009, Spain.
Fundación ARAID, Government of Aragón, Zaragoza 50018, Spain.
Department Abiotic Stress, Instituto de Recursos Naturales y Agrobiología (IRNASA-CSIC), Cordel de Merinas 40-52, Salamanca 37008, Spain.
Computational Systems Biology Group, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Madrid 28049, Spain.
Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), Campus Miguel de Unamuno, Salamanca 37007, Spain.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.77 kDa 
• Atom Count: 6,545 
• Modeled Residue Count: 774 
• Deposited Residue Count: 826 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase	A, B	413	Eremothecium gossypii ATCC 10895	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5GP	C [auth A], D [auth A], G [auth B], H [auth B]	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N
GOL	F [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	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 (Depositor), 0.152 (DCC) 
• R-Value Work:  0.124 (Depositor), 0.131 (DCC) 
• R-Value Observed: 0.125 (Depositor) 

Space Group: P 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.48	α = 90
b = 117.48	β = 90
c = 56.525	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-25 
Deposition Author(s): Buey, R.M., de Pereda, J.M., Revuelta, J.L.

Revision History  

• 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