8QZV | pdb_00008qzv

Crystal structure of translation factor eIF5A from Trichomonas vaginalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.236 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural characterization of the (deoxy)hypusination in Trichomonas vaginalis questions the bifunctionality of deoxyhypusine synthase.

Wator, E.Wilk, P.Kochanowski, P.Grudnik, P.

(2024) FEBS J 291: 3856-3869

  • DOI: https://doi.org/10.1111/febs.17207
  • Primary Citation Related Structures: 
    8QZV, 8QZW, 8QZX

  • PubMed Abstract: 

    Trichomonas vaginalis, the causative agent of trichomoniasis, is a prevalent anaerobic protozoan parasite responsible for the most common nonviral sexually transmitted infection globally. While metronidazole and its derivatives are approved drugs for this infection, rising resistance necessitates the exploration of new antiparasitic therapies. Protein posttranslational modifications (PTMs) play crucial roles in cellular processes, and among them, hypusination, involving eukaryotic translation factor 5A (eIF5A), has profound implications. Despite extensive studies in various organisms, the role of hypusination in T. vaginalis and its potential impact on parasite biology and pathogenicity remain poorly understood. This study aims to unravel the structural basis of the hypusination pathway in T. vaginalis using X-ray crystallography and cryo-electron microscopy. The results reveal high structural homology between T. vaginalis and human orthologs, providing insights into the molecular architecture of eIF5A and deoxyhypusine synthase (DHS) and their interaction. Contrary to previous suggestions of bifunctionality, our analyses indicate that the putative hydroxylation site in tvDHS is nonfunctional, and biochemical assays demonstrate exclusive deoxyhypusination capability. These findings challenge the notion of tvDHS functioning as both deoxyhypusine synthase and hydroxylase. The study enhances understanding of the hypusination pathway in T. vaginalis, shedding light on its functional relevance and potential as a drug target, and contributing to the development of novel therapeutic strategies against trichomoniasis.


  • Organizational Affiliation
    • Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.

Macromolecule Content 

  • Total Structure Weight: 18.43 kDa 
  • Atom Count: 1,201 
  • Modeled Residue Count: 137 
  • Deposited Residue Count: 167 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 5A167Trichomonas vaginalisMutation(s): 0 
Gene Names: eIF-5A1
UniProt
Find proteins for D5MC19 (Trichomonas vaginalis)
Explore D5MC19 
Go to UniProtKB:  D5MC19
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5MC19
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.236 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.262α = 90
b = 40.795β = 90
c = 117.024γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2019/35/N/NZ1/02805
Polish National Science CentrePoland2019/33/B/NZ1/01839

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-03
    Type: Initial release
  • Version 1.1: 2024-07-10
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Database references, Structure summary