tRNA guanine transglycosylase (TGT) in complex with Furanoside-Based lin-Benzoguanine 1

Experimental Data Snapshot

  • Resolution: 1.41 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.124 

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Replacement of Water Molecules in a Phosphate Binding Site by Furanoside-Appended lin-Benzoguanine Ligands of tRNA-Guanine Transglycosylase (TGT).

Barandun, L.J.Ehrmann, F.R.Zimmerli, D.Immekus, F.Giroud, M.Grunenfelder, C.Schweizer, W.B.Bernet, B.Betz, M.Heine, A.Klebe, G.Diederich, F.

(2015) Chemistry 21: 126-135

  • DOI: https://doi.org/10.1002/chem.201405764
  • Primary Citation of Related Structures:  
    4KWO, 4LBU, 4LEQ

  • PubMed Abstract: 

    The enzyme tRNA-guanine transglycosylase has been identified as a drug target for the foodborne illness shigellosis. A key challenge in structure-based design for this enzyme is the filling of the polar ribose-34 pocket. Herein, we describe a novel series of ligands consisting of furanoside-appended lin-benzoguanines. They were designed to replace a conserved water cluster and differ by the functional groups at C(2) and C(3) of the furanosyl moiety being either OH or OMe. The unfavorable desolvation of Asp102 and Asp280, which are located close to the ribose-34 pocket, had a significant impact on binding affinity. While the enzyme has tRNA as its natural substrate, X-ray co-crystal structures revealed that the furanosyl moieties of the ligands are not accommodated in the tRNA ribose-34 site, but at the location of the adjacent phosphate group. A remarkable similarity of the position of the oxygen atoms in these two structures suggests furanosides as a potential phosphate isoster.

  • Organizational Affiliation

    Laboratorium für Organische Chemie, ETH Zürich, Vladimir-Prelog-Weg 3, HCI, 8093 Zürich (Switzerland), Fax: (+41) 44-632-1109.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Queuine tRNA-ribosyltransferase388Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821Mutation(s): 0 
Gene Names: tgtZMO0363
Find proteins for P28720 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4))
Explore P28720 
Go to UniProtKB:  P28720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28720
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
1WK Binding MOAD:  4LEQ Kd: 288 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.41 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.124 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.623α = 90
b = 65.106β = 96.3
c = 70.357γ = 90
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: 2014-12-24
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description