Structure of human IMP dehydrogenase, isoform 2, bound to GDP

Experimental Data Snapshot

  • Resolution: 2.57 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


A Nucleotide-Dependent Conformational Switch Controls the Polymerization of Human IMP Dehydrogenases to Modulate their Catalytic Activity.

Fernandez-Justel, D.Nunez, R.Martin-Benito, J.Jimeno, D.Gonzalez-Lopez, A.Soriano, E.M.Revuelta, J.L.Buey, R.M.

(2019) J Mol Biol 431: 956-969

  • DOI: https://doi.org/10.1016/j.jmb.2019.01.020
  • Primary Citation of Related Structures:  
    6I0M, 6I0O

  • PubMed Abstract: 

    Inosine 5'-monophosphate dehydrogenase (IMPDH) catalyzes the rate-limiting step in the de novo GTP biosynthetic pathway and plays essential roles in cell proliferation. As a clinical target, IMPDH has been studied for decades, but it has only been within the last years that we are starting to understand the complexity of the mechanisms of its physiological regulation. Here, we report structural and functional insights into how adenine and guanine nucleotides control a conformational switch that modulates the assembly of the two human IMPDH enzymes into cytoophidia and allosterically regulates their catalytic activity. In vitro reconstituted micron-length cytoophidia-like structures show catalytic activity comparable to unassembled IMPDH but, in turn, are more resistant to GTP/GDP allosteric inhibition. Therefore, IMPDH cytoophidia formation facilitates the accumulation of high levels of guanine nucleotides when the cell requires it. Finally, we demonstrate that most of the IMPDH retinopathy-associated mutations abrogate GTP/GDP-induced allosteric inhibition and alter cytoophidia dynamics.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase 2
A, B
517Homo sapiensMutation(s): 0 
Gene Names: IMPDH2IMPD2
UniProt & NIH Common Fund Data Resources
Find proteins for P12268 (Homo sapiens)
Explore P12268 
Go to UniProtKB:  P12268
PHAROS:  P12268
GTEx:  ENSG00000178035 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12268
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GDP

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
O [auth B]
P [auth B]
D [auth A],
E [auth A],
F [auth A],
O [auth B],
P [auth B],
Q [auth B]
C10 H15 N5 O11 P2
Query on 5GP

Download Ideal Coordinates CCD File 
C [auth A],
N [auth B]
C10 H14 N5 O8 P
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
R [auth B],
S [auth B],
T [auth B]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.57 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.220 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.729α = 90
b = 134.729β = 90
c = 324.081γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
STARANISOdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description