Adenosine/guanosine nucleoside hydrolase bound to a fragment inhibitor

Experimental Data Snapshot

  • Resolution: 2.33 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

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This is version 1.2 of the entry. See complete history


Structure-Guided Insight into the Specificity and Mechanism of a Parasitic Nucleoside Hydrolase.

Muellers, S.N.Nyitray, M.M.Reynarowych, N.Saljanin, E.Benzie, A.L.Schoenfeld, A.R.Stockman, B.J.Allen, K.N.

(2022) Biochemistry 61: 1853-1861

  • DOI: https://doi.org/10.1021/acs.biochem.2c00361
  • Primary Citation of Related Structures:  
    8DB6, 8DB7, 8DB8, 8DB9

  • PubMed Abstract: 

    Trichomonas vaginalis is the causative parasitic protozoan of the disease trichomoniasis, the most prevalent, nonviral sexually transmitted disease in the world. T. vaginalis is a parasite that scavenges nucleosides from the host organism via catalysis by nucleoside hydrolase (NH) enzymes to yield purine and pyrimidine bases. One of the four NH enzymes identified within the genome of T. vaginalis displays unique specificity toward purine nucleosides, adenosine and guanosine, but not inosine, and atypically shares greater sequence similarity to the pyrimidine hydrolases. Bioinformatic analysis of this enzyme, adenosine/guanosine-preferring nucleoside ribohydrolase (AGNH), was incapable of identifying the residues responsible for this uncommon specificity, highlighting the need for structural information. Here, we report the X-ray crystal structures of holo , unliganded AGNH and three additional structures of the enzyme bound to fragment and small-molecule inhibitors. Taken together, these structures facilitated the identification of residue Asp231, which engages in substrate interactions in the absence of those residues that typically support the canonical purine-specific tryptophan-stacking specificity motif. An altered substrate-binding pose is mirrored by repositioning within the protein scaffold of the His80 general acid/base catalyst. The newly defined structure-determined sequence markers allowed the assignment of additional NH orthologs, which are proposed to exhibit the same specificity for adenosine and guanosine alone and further delineate specificity classes for these enzymes.

  • Organizational Affiliation

    Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-uridine preferring nucleoside hydrolase family proteinA [auth B],
B [auth A],
304Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_213720
Find proteins for A2EYV3 (Trichomonas vaginalis (strain ATCC PRA-98 / G3))
Explore A2EYV3 
Go to UniProtKB:  A2EYV3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2EYV3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
R2O (Subject of Investigation/LOI)
Query on R2O

Download Ideal Coordinates CCD File 
F [auth B],
K [auth C],
N [auth D]
C9 H10 F N3
Query on GOL

Download Ideal Coordinates CCD File 
E [auth B],
H [auth A],
J [auth C],
M [auth D]
C3 H8 O3
Query on CA

Download Ideal Coordinates CCD File 
G [auth B],
I [auth A],
L [auth C],
O [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.33 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.651α = 83.019
b = 74.537β = 80.897
c = 85.641γ = 89.9
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
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: 2022-09-07
    Type: Initial release
  • Version 1.1: 2022-09-14
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Refinement description