5MCP

Structure of IMP dehydrogenase from Ashbya gossypii bound to ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases.

Buey, R.M.Fernandez-Justel, D.Marcos-Alcalde, I.Winter, G.Gomez-Puertas, P.de Pereda, J.M.Luis Revuelta, J.

(2017) Sci Rep 7: 2648-2648

  • DOI: 10.1038/s41598-017-02805-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Inosine-5'-monophosphate dehydrogenase (IMPDH) is an essential enzyme for nucleotide metabolism and cell proliferation. Despite IMPDH is the target of drugs with antiviral, immunosuppressive and antitumor activities, its physiological mechanisms of r ...

    Inosine-5'-monophosphate dehydrogenase (IMPDH) is an essential enzyme for nucleotide metabolism and cell proliferation. Despite IMPDH is the target of drugs with antiviral, immunosuppressive and antitumor activities, its physiological mechanisms of regulation remain largely unknown. Using the enzyme from the industrial fungus Ashbya gossypii, we demonstrate that the binding of adenine and guanine nucleotides to the canonical nucleotide binding sites of the regulatory Bateman domain induces different enzyme conformations with significantly distinct catalytic activities. Thereby, the comparison of their high-resolution structures defines the mechanistic and structural details of a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity of eukaryotic IMPDHs. Remarkably, retinopathy-associated mutations lie within the mechanical hinges of the conformational change, highlighting its physiological relevance. Our results expand the mechanistic repertoire of Bateman domains and pave the road to new approaches targeting IMPDHs.


    Organizational Affiliation

    Metabolic Engineering Group, Dpto. Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain. ruben.martinez@usal.es.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inosine-5'-monophosphate dehydrogenase
A, B, C, D, E, F, G, H
523Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)Mutation(s): 0 
EC: 1.1.1.205
Find proteins for Q756Z6 (Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056))
Go to UniProtKB:  Q756Z6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, C, D, E, F, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.249 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 127.891α = 90.00
b = 152.090β = 93.03
c = 152.255γ = 90.00
Software Package:
Software NamePurpose
DIALSdata scaling
PHASERphasing
PHENIXrefinement
DIALSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2016-79237-P

Revision History 

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence, Derived calculations
  • Version 1.2: 2018-01-24
    Type: Source and taxonomy