5MCP

Structure of IMP dehydrogenase from Ashbya gossypii bound to ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1038/s41598-017-02805-x
  • Primary Citation of Related Structures:  
    5MCP, 5TC3

  • 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 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. [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H
523Eremothecium 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth E]
FA [auth F]
HA [auth G]
AA [auth E],
BA [auth E],
CA [auth E],
FA [auth F],
HA [auth G],
I [auth A],
IA [auth G],
J [auth A],
JA [auth G],
K [auth A],
L [auth B],
LA [auth H],
M [auth B],
MA [auth H],
N [auth B],
NA [auth H],
P [auth B],
Q [auth B],
R [auth C],
S [auth C],
T [auth C],
W [auth D],
X [auth D],
Y [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
DA [auth E]
EA [auth E]
GA [auth F]
KA [auth G]
O [auth B]
DA [auth E],
EA [auth E],
GA [auth F],
KA [auth G],
O [auth B],
U [auth C],
V [auth C],
Z [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.251 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.891α = 90
b = 152.09β = 93.03
c = 152.255γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description