1ENU | pdb_00001enu

A new target for shigellosis: Rational design and crystallographic studies of inhibitors of tRNA-guanine transglycosylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.211 (Depositor) 
  • R-Value Work: 
    0.176 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

A new target for shigellosis: rational design and crystallographic studies of inhibitors of tRNA-guanine transglycosylase.

Gradler, U.Gerber, H.D.Goodenough-Lashua, D.M.Garcia, G.A.Ficner, R.Reuter, K.Stubbs, M.T.Klebe, G.

(2001) J Mol Biology 306: 455-467

  • DOI: https://doi.org/10.1006/jmbi.2000.4256
  • Primary Citation Related Structures: 
    1ENU, 1F3E

  • PubMed Abstract: 

    Eubacterial tRNA-guanine transglycosylase (TGT) is involved in the hyper-modification of cognate tRNAs leading to the exchange of G34 at the wobble position in the anticodon loop by preQ1 (2-amino-5-(aminomethyl)pyrrolo[2,3-d]pyrimidin-4(3H)-one) as part of the biosynthesis of queuine (Q). Mutation of the tgt gene in Shigella flexneri results in a significant loss of pathogenicity of the bacterium, revealing TGT as a new target for the design of potent drugs against Shigellosis. The X-ray structure of Zymomonas mobilis TGT in complex with preQ1 was used to search for new putative inhibitors with the computer program LUDI. An initial screen of the Available Chemical Directory, a database compiled from commercially available compounds, suggested several hits. Of these, 4-aminophthalhydrazide (APH) showed an inhibition constant in the low micromolar range. The 1.95 A crystal structure of APH in complex with Z. mobilis TGT served as a starting point for further modification of this initial lead.


  • Organizational Affiliation
    • Institut für Pharmazeutische Chemie, Marbacher Weg 6, Philipps-Universität Marburg, 35032, Germany.

Macromolecule Content 

  • Total Structure Weight: 43.17 kDa 
  • Atom Count: 3,372 
  • Modeled Residue Count: 372 
  • Deposited Residue Count: 386 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TRNA-GUANINE TRANSGLYCOSYLASE386Zymomonas mobilisMutation(s): 0 
EC: 2.4.2.29
UniProt
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
Expand
Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
APZ BindingDB:  1ENU Ki: 8300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.211 (Depositor) 
  • R-Value Work:  0.176 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.79α = 90
b = 64.96β = 96.47
c = 70.42γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-04-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-10-03
    Changes: Advisory, Data collection
  • Version 1.4: 2020-08-19
    Changes: Advisory, Derived calculations
  • Version 1.5: 2024-02-07
    Changes: Advisory, Data collection, Database references