4AF0

Crystal structure of cryptococcal inosine monophosphate dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

De Novo GTP Biosynthesis is Critical for Virulence of the Fungal Pathogen Cryptococcus Neoformans

Morrow, C.A.Valkov, E.Stamp, A.Chow, E.W.L.Lee, I.R.Wronski, A.Williams, S.J.Hill, J.M.Djordjevic, J.T.Kappler, U.Kobe, B.Fraser, J.A.

(2012) Plos Pathog. 8: 2957

  • DOI: 10.1371/journal.ppat.1002957

  • PubMed Abstract: 
  • We have investigated the potential of the GTP synthesis pathways as chemotherapeutic targets in the human pathogen Cryptococcus neoformans, a common cause of fatal fungal meningoencephalitis. We find that de novo GTP biosynthesis, but not the alterna ...

    We have investigated the potential of the GTP synthesis pathways as chemotherapeutic targets in the human pathogen Cryptococcus neoformans, a common cause of fatal fungal meningoencephalitis. We find that de novo GTP biosynthesis, but not the alternate salvage pathway, is critical to cryptococcal dissemination and survival in vivo. Loss of inosine monophosphate dehydrogenase (IMPDH) in the de novo pathway results in slow growth and virulence factor defects, while loss of the cognate phosphoribosyltransferase in the salvage pathway yielded no phenotypes. Further, the Cryptococcus species complex displays variable sensitivity to the IMPDH inhibitor mycophenolic acid, and we uncover a rare drug-resistant subtype of C. gattii that suggests an adaptive response to microbial IMPDH inhibitors in its environmental niche. We report the structural and functional characterization of IMPDH from Cryptococcus, revealing insights into the basis for drug resistance and suggesting strategies for the development of fungal-specific inhibitors. The crystal structure reveals the position of the IMPDH moveable flap and catalytic arginine in the open conformation for the first time, plus unique, exploitable differences in the highly conserved active site. Treatment with mycophenolic acid led to significantly increased survival times in a nematode model, validating de novo GTP biosynthesis as an antifungal target in Cryptococcus.


    Organizational Affiliation

    Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
A
556Cryptococcus neoformansMutation(s): 0 
Gene Names: IMD1
EC: 1.1.1.205
Find proteins for E3P6S0 (Cryptococcus neoformans)
Go to UniProtKB:  E3P6S0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
B
556Cryptococcus neoformansMutation(s): 0 
Gene Names: IMD1
EC: 1.1.1.205
Find proteins for E3P6S0 (Cryptococcus neoformans)
Go to UniProtKB:  E3P6S0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMP
Query on IMP

Download SDF File 
Download CCD File 
A, B
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MOA
Query on MOA

Download SDF File 
Download CCD File 
A, B
MYCOPHENOLIC ACID
6-(1,3-DIHYDRO-7-HYDROXY-5-METHOXY-4-METHYL-1-OXOISOBENZOFURAN-6-YL)-4-METHYL-4-HEXANOIC ACID
C17 H20 O6
HPNSFSBZBAHARI-RUDMXATFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MOAKi: 198 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.173 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 149.630α = 90.00
b = 149.630β = 90.00
c = 122.700γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
BUSTERrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2012-11-21
    Type: Database references