4DXX

TGT K52M mutant crystallized at pH 8.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Hot-spot analysis to dissect the functional protein-protein interface of a tRNA-modifying enzyme.

Jakobi, S.Nguyen, T.X.Debaene, F.Metz, A.Sanglier-Cianferani, S.Reuter, K.Klebe, G.

(2014) Proteins 82: 2713-2732

  • DOI: 10.1002/prot.24637
  • Primary Citation of Related Structures:  3UNT, 3UVI

  • PubMed Abstract: 
  • Interference with protein-protein interactions of interfaces larger than 1500 Ų by small drug-like molecules is notoriously difficult, particularly if targeting homodimers. The tRNA modifying enzyme Tgt is only functionally active as a homodimer. Th ...

    Interference with protein-protein interactions of interfaces larger than 1500 Ų by small drug-like molecules is notoriously difficult, particularly if targeting homodimers. The tRNA modifying enzyme Tgt is only functionally active as a homodimer. Thus, blocking Tgt dimerization is a promising strategy for drug therapy as this protein is key to the development of Shigellosis. Our goal was to identify hot-spot residues which, upon mutation, result in a predominantly monomeric state of Tgt. The detailed understanding of the spatial location and stability contribution of the individual interaction hot-spot residues and the plasticity of motifs involved in the interface formation is a crucial prerequisite for the rational identification of drug-like inhibitors addressing the respective dimerization interface. Using computational analyses, we identified hot-spot residues that contribute particularly to dimer stability: a cluster of hydrophobic and aromatic residues as well as several salt bridges. This in silico prediction led to the identification of a promising double mutant, which was validated experimentally. Native nano-ESI mass spectrometry showed that the dimerization of the suggested mutant is largely prevented resulting in a predominantly monomeric state. Crystal structure analysis and enzyme kinetics of the mutant variant further support the evidence for enhanced monomerization and provide first insights into the structural consequences of the dimer destabilization.


    Organizational Affiliation

    Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032, Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Queuine tRNA-ribosyltransferase
A
386Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)Gene Names: tgt
EC: 2.4.2.29
Find proteins for P28720 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4))
Go to UniProtKB:  P28720
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 91.220α = 90.00
b = 64.865β = 95.99
c = 70.082γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
MAR345dtbdata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2014-07-16
    Type: Database references
  • Version 1.2: 2014-10-15
    Type: Database references
  • Version 1.3: 2017-10-25
    Type: Author supporting evidence