8OIA

Trichomonas vaginalis riboside hydrolase in complex with D-ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.234 

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


Literature

A riboside hydrolase that salvages both nucleobases and nicotinamide in the auxotrophic parasite Trichomonas vaginalis.

Patrone, M.Galasyn, G.S.Kerin, F.Nyitray, M.M.Parkin, D.W.Stockman, B.J.Degano, M.

(2023) J Biol Chem 299: 105077-105077

  • DOI: https://doi.org/10.1016/j.jbc.2023.105077
  • Primary Citation of Related Structures:  
    8OI7, 8OI9, 8OIA, 8OIB, 8OIC

  • PubMed Abstract: 

    Pathogenic parasites of the Trichomonas genus are causative agents of sexually transmitted diseases affecting millions of individuals worldwide and whose outcome may include stillbirths and enhanced cancer risks and susceptibility to HIV infection. Trichomonas vaginalis relies on imported purine and pyrimidine nucleosides and nucleobases for survival, since it lacks the enzymatic activities necessary for de novo biosynthesis. Here we show that T. vaginalis additionally lacks homologues of the bacterial or mammalian enzymes required for the synthesis of the nicotinamide ring, a crucial component in the redox cofactors NAD + and NADP. Moreover, we show that a yet fully uncharacterized T. vaginalis protein homologous to bacterial and protozoan nucleoside hydrolases is active as a pyrimidine nucleosidase but shows the highest specificity toward the NAD + metabolite nicotinamide riboside. Crystal structures of the trichomonal riboside hydrolase in different states reveals novel intermediates along the nucleoside hydrolase-catalyzed hydrolytic reaction, including an unexpected asymmetry in the homotetrameric assembly. The active site structure explains the broad specificity toward different ribosides and offers precise insights for the engineering of specific inhibitors that may simultaneously target different essential pathways in the parasite.


  • Organizational Affiliation

    Biocrystallography Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milano, Italy; Faculty of Medicine and Surgery, Università Vita-Salute San Raffaele, Milano, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-uridine preferring nucleoside hydrolase family protein
A, B, C, D
347Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_092730
UniProt
Find proteins for A2FTT0 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
Explore A2FTT0 
Go to UniProtKB:  A2FTT0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2FTT0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
M [auth C]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
RIB (Subject of Investigation/LOI)
Query on RIB

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C],
P [auth D]
alpha-D-ribofuranose
C5 H10 O5
HMFHBZSHGGEWLO-AIHAYLRMSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
N [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
K [auth C],
O [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.995α = 90
b = 135.622β = 104.691
c = 94.075γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Association for Cancer ResearchItalyIG25764
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR15AI128585

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-02
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Data collection, Database references