Pyridoxal kinase of Entamoeba histolytica with ADP

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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Characterization and functional insights into the Entamoeba histolytica pyridoxal kinase, an enzyme essential for its survival.

Tarique, K.F.Devi, S.Tomar, P.Ali, M.F.Rehman, S.A.A.Gourinath, S.

(2020) J Struct Biol 212: 107645-107645

  • DOI: https://doi.org/10.1016/j.jsb.2020.107645
  • Primary Citation of Related Structures:  
    4S1H, 4S1I, 4S1M

  • PubMed Abstract: 

    Pyridoxal 5'-phosphate (PLP) is the active form of vitamin B 6 and a cofactor for more than 140 enzymes. This coenzyme plays a pivotal role in catalysis of various enzymatic reactions that are critical for the survival of organisms. Entamoeba histolytica depends on the uptake of pyridoxal (PL), a B 6 vitamer from the external environment which is then phosphorylated by pyridoxal kinase (EhPLK) to form PLP via the salvage pathway. E. histolytica cannot synthesise vitamin B 6 de-novo, and also lacks pyridoxine 5'-phosphate oxidase, a salvage pathway enzyme required to produce PLP from pyridoxine phosphate (PNP) and pyridoxamine phosphate (PMP). Analysing the importance of PLK in E. histolytica, we have determined the high-resolution crystal structures of the dimeric pyridoxal kinase in apo, ADP-bound, and PLP-bound states. These structures provided a snapshot of the transition state and help in understanding the reaction mechanism in greater detail. The EhPLK structure significantly differed from the human homologue at its PLP binding site, and the phylogenetic study also revealed its divergence from human PLK. Further, gene regulation of EhPLK using sense and antisense RNA showed that any change in optimal level is harmful to the pathogen. Biochemical and in vivo studies unveiled EhPLK to be essential for this pathogen, while the molecular differences with human PLK structure can be exploited for the structure-guided design of EhPLK inhibitors.

  • Organizational Affiliation

    Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India; Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxal kinase
A, B
287Entamoeba histolyticaMutation(s): 0 
Gene Names: EHI_126090
Find proteins for C4LVZ4 (Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM))
Explore C4LVZ4 
Go to UniProtKB:  C4LVZ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC4LVZ4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.256α = 89.94
b = 44.272β = 102.89
c = 75.246γ = 107.03
Software Package:
Software NamePurpose
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data 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: 2015-01-28
    Type: Initial release
  • Version 1.1: 2021-03-24
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-04-03
    Changes: Refinement description