6AJE

Crystal structure of DHODH in complex with ferulenol from Eimeria tenella


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.225 

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This is version 1.1 of the entry. See complete history


Literature

Structural and Biochemical Features of Eimeria tenella Dihydroorotate Dehydrogenase, a Potential Drug Target.

Sato, D.Hartuti, E.D.Inaoka, D.K.Sakura, T.Amalia, E.Nagahama, M.Yoshioka, Y.Tsuji, N.Nozaki, T.Kita, K.Harada, S.Matsubayashi, M.Shiba, T.

(2020) Genes (Basel) 11

  • DOI: 10.3390/genes11121468
  • Primary Citation of Related Structures:  
    6AJ5, 6AJE, 6IDJ

  • PubMed Abstract: 
  • Dihydroorotate dehydrogenase (DHODH) is a mitochondrial monotopic membrane protein that plays an essential role in the pyrimidine de novo biosynthesis and electron transport chain pathways. In Eimeria tenella , an intracellular apicomplexan parasite that causes the most severe form of chicken coccidiosis, the activity of pyrimidine salvage pathway at the intracellular stage is negligible and it relies on the pyrimidine de novo biosynthesis pathway ...

    Dihydroorotate dehydrogenase (DHODH) is a mitochondrial monotopic membrane protein that plays an essential role in the pyrimidine de novo biosynthesis and electron transport chain pathways. In Eimeria tenella , an intracellular apicomplexan parasite that causes the most severe form of chicken coccidiosis, the activity of pyrimidine salvage pathway at the intracellular stage is negligible and it relies on the pyrimidine de novo biosynthesis pathway. Therefore, the enzymes of the de novo pathway are considered potential drug target candidates for the design of compounds with activity against this parasite. Although, DHODHs from E. tenella (EtDHODH), Plasmodium falciparum (PfDHODH), and human (HsDHODH) show distinct sensitivities to classical DHODH inhibitors, in this paper, we identify ferulenol as a potent inhibitor of both EtDHODH and HsDHODH. Additionally, we report the crystal structures of EtDHODH and HsDHODH in the absence and presence of ferulenol. Comparison of these enzymes showed that despite similar overall structures, the EtDHODH has a long insertion in the N-terminal helix region that assumes a disordered configuration. In addition, the crystal structures revealed that the ferulenol binding pocket of EtDHODH is larger than that of HsDHODH. These differences can be explored to accelerate structure-based design of inhibitors specifically targeting EtDHODH.


    Organizational Affiliation

    Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydroorotate dehydrogenase (quinone), mitochondrialA, B, C, D436Eimeria tenellaMutation(s): 0 
Gene Names: ETH_00004975
EC: 1.3.5.2
Membrane Entity: Yes 
UniProt
Find proteins for U6KL66 (Eimeria tenella)
Explore U6KL66 
Go to UniProtKB:  U6KL66
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupU6KL66
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.65 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.225 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.984α = 90
b = 132.984β = 90
c = 214.998γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references