Acanthamoeba IGPD in complex with R-C348 to 1.7A resolution

Experimental Data Snapshot

  • Resolution: 1.79 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

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Structural and functional studies of histidine biosynthesis in Acanthamoeba spp. demonstrates a novel molecular arrangement and target for antimicrobials.

Rice, C.A.Campbell, S.J.Bisson, C.Owen, H.J.Sedelnikova, S.E.Baker, P.J.Rice, D.W.Henriquez, F.L.Roberts, C.W.

(2018) PLoS One 13: e0198827-e0198827

  • DOI: https://doi.org/10.1371/journal.pone.0198827
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Acanthamoeba is normally free-living, but sometimes facultative and occasionally opportunistic parasites. Current therapies are, by necessity, arduous and yet poorly effective due to their inabilities to kill cyst stages or in some cases to actually induce encystation. Acanthamoeba can therefore survive as cysts and cause disease recurrence. Herein, in pursuit of better therapies and to understand the biochemistry of this understudied organism, we characterize its histidine biosynthesis pathway and explore the potential of targeting this with antimicrobials. We demonstrate that Acanthamoeba is a histidine autotroph, but with the ability to scavenge preformed histidine. It is able to grow in defined media lacking this amino acid, but is inhibited by 3-amino-1,2,4-triazole (3AT) that targets Imidazoleglycerol-Phosphate Dehydratase (IGPD) the rate limiting step of histidine biosynthesis. The structure of Acanthamoeba IGPD has also been determined in complex with 2-hydroxy-3-(1,2,4-triazol-1-yl) propylphosphonate [(R)-C348], a recently described novel inhibitor of Arabidopsis thaliana IGPD. This compound inhibited the growth of four Acanthamoeba species, having a 50% inhibitory concentration (IC50) ranging from 250-526 nM. This effect could be ablated by the addition of 1 mM exogenous free histidine, but importantly not by physiological concentrations found in mammalian tissues. The ability of 3AT and (R)-C348 to restrict the growth of four strains of Acanthamoeba spp. including a recently isolated clinical strain, while not inducing encystment, demonstrates the potential therapeutic utility of targeting the histidine biosynthesis pathway in Acanthamoeba.

  • Organizational Affiliation

    Institute of Biomedical and Environmental Health Research, School of Science and Sport, University of West of Scotland, Paisley, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Imidazoleglycerol-phosphate dehydratase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
197Acanthamoeba castellaniiMutation(s): 0 
Find proteins for L8H477 (Acanthamoeba castellanii (strain ATCC 30010 / Neff))
Explore L8H477 
Go to UniProtKB:  L8H477
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL8H477
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5LD

Download Ideal Coordinates CCD File 
AA [auth E]
DA [auth F]
JA [auth H]
LA [auth I]
NA [auth J]
AA [auth E],
DA [auth F],
JA [auth H],
LA [auth I],
NA [auth J],
O [auth A],
R [auth B],
RA [auth K],
S [auth B],
VA [auth L],
W [auth C],
Y [auth D]
[(2R)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]phosphonic acid
C5 H10 N3 O4 P
Query on MN

Download Ideal Coordinates CCD File 
BA [auth F]
CA [auth F]
EA [auth G]
FA [auth G]
GA [auth H]
BA [auth F],
CA [auth F],
EA [auth G],
FA [auth G],
GA [auth H],
HA [auth H],
IA [auth H],
KA [auth I],
M [auth A],
MA [auth J],
N [auth A],
OA [auth K],
P [auth B],
PA [auth K],
Q [auth B],
QA [auth K],
SA [auth L],
T [auth C],
TA [auth L],
U [auth C],
UA [auth L],
V [auth C],
X [auth D],
Z [auth E]
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.79 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.69α = 90
b = 156.1β = 125.42
c = 117.12γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description