5ZEE

Crystal structure of Entamoeba histolytica Arginase in complex with N(omega)-hydroxy-L-arginine (NOHA) at 1.74 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

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Literature

Structural insights into Entamoeba histolytica arginase and structure-based identification of novel non-amino acid based inhibitors as potential antiamoebic molecules.

Malik, A.Dalal, V.Ankri, S.Tomar, S.

(2019) FEBS J 286: 4135-4155

  • DOI: 10.1111/febs.14960
  • Primary Citation of Related Structures:  
    5ZEH, 5ZEE, 5ZEF

  • PubMed Abstract: 
  • Arginase, the binuclear metalloenzyme, is a potential target for therapeutic intervention in protozoan infections. Entamoeba histolytica infection causes amebiasis which is the second most common cause of protozoan-related human deaths after malaria. Here, we report the crystal structure of E ...

    Arginase, the binuclear metalloenzyme, is a potential target for therapeutic intervention in protozoan infections. Entamoeba histolytica infection causes amebiasis which is the second most common cause of protozoan-related human deaths after malaria. Here, we report the crystal structure of E. histolytica arginase (EhArg) in complex with two known inhibitors N ω -hydroxy-l-arginine (l-NOHA) and l-norvaline, and its product l-ornithine at 1.7, 2.0, and 2.4 Å, respectively. Structural and comparative analysis of EhArg-inhibitor complexes with human arginase revealed that despite only 33% sequence identity, the structural determinants of inhibitor recognition and binding are highly conserved in arginases with variation in oligomerization motifs. Knowledge regarding the spatial organization of residues making molecular contacts with inhibitory compounds enabled in the identification of four novel non-amino acid inhibitors, namely irinotecan, argatroban, cortisone acetate, and sorafenib. In vitro testing of the in silico-identified inhibitors using purified enzyme proved that irinotecan, argatroban, cortisone acetate, and sorafenib inhibit EhArg with IC 50 value (mm) of 1.99, 2.40, 0.91, and 2.75, respectively, as compared to the known inhibitors l-NOHA and l-norvaline with IC 50 value (mm) of 1.57 and 17.9, respectively. The identification of structure-based non-amino acid inhibitory molecules against arginase will be constructive in design and discovery of novel chemical modulators for treating amebiasis by directed therapeutics.


    Organizational Affiliation

    Department of Biotechnology, Indian Institute of Technology Roorkee, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ArginaseA, B312Entamoeba histolyticaMutation(s): 0 
Gene Names: EHI_152330
EC: 3.5.3.1
UniProt
Find proteins for C4LSS0 (Entamoeba histolytica)
Explore C4LSS0 
Go to UniProtKB:  C4LSS0
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.722α = 90
b = 97.538β = 90
c = 125.067γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references