6KR5

Crystal structure of O-Acetyl Serine Sulfhydrylase isoform 3 from Entamoeba histolytica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of O-Acetylserine sulfhydralase (OASS) isoform 3 from Entamoeba histolytica: Pharmacophore-based virtual screening and validation of novel inhibitors.

Dharavath, S.Vijayan, R.Kumari, K.Tomar, P.Gourinath, S.

(2020) Eur J Med Chem 192: 112157-112157

  • DOI: https://doi.org/10.1016/j.ejmech.2020.112157
  • Primary Citation of Related Structures:  
    6KR5

  • PubMed Abstract: 

    The l-cysteine is crucial for growth, survival, defense against oxidative stress, and pathogenesis of Entamoeba histolytica. The de novo biosynthesis of l-cysteine in E. histolytica, has a two-step pathway, where O-acetylserine sulfhydrylase (OASS) catalyses the last step by converting OAS to l-cysteine. This pathway is absent in humans and hence represents a promising target for novel therapeutics. E. histolytica expresses three isoforms of OASS and knockdown studies showed the importance of these enzymes for the survival of the pathogen. Here, we report the crystal structure of OASS isoform 3 from E. histolytica to 1.54 Å resolution. The active site geometries and kinetics of EhOASS3 and EhOASS1 structures were found to be very similar. Small-molecule libraries were screened against EhOASS3 and compounds were shortlisted based on the docking scores. F3226-1387 showed best inhibition with IC 50 of 38 μM against EhOASS3 and was able to inhibit the growth of the organism to 72%.


  • Organizational Affiliation

    School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine synthase 3
A, B
338Entamoeba histolyticaMutation(s): 0 
Gene Names: CS 3CL6EHI_060340EHI_060340
EC: 2.5.1.47
UniProt
Find proteins for Q401L7 (Entamoeba histolytica)
Explore Q401L7 
Go to UniProtKB:  Q401L7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ401L7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.505α = 90
b = 85.874β = 90
c = 91.164γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-09
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description