5TCF

Crystal structure of tryptophan synthase from M. tuberculosis - ligand-free form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A small-molecule allosteric inhibitor of Mycobacterium tuberculosis tryptophan synthase.

Wellington, S.Nag, P.P.Michalska, K.Johnston, S.E.Jedrzejczak, R.P.Kaushik, V.K.Clatworthy, A.E.Siddiqi, N.McCarren, P.Bajrami, B.Maltseva, N.I.Combs, S.Fisher, S.L.Joachimiak, A.Schreiber, S.L.Hung, D.T.

(2017) Nat. Chem. Biol. 13: 943-950

  • DOI: 10.1038/nchembio.2420
  • Primary Citation of Related Structures:  5TCG, 5TCH, 5TCI, 5TCJ

  • PubMed Abstract: 
  • New antibiotics with novel targets are greatly needed. Bacteria have numerous essential functions, but only a small fraction of such processes-primarily those involved in macromolecular synthesis-are inhibited by current drugs. Targeting metabolic en ...

    New antibiotics with novel targets are greatly needed. Bacteria have numerous essential functions, but only a small fraction of such processes-primarily those involved in macromolecular synthesis-are inhibited by current drugs. Targeting metabolic enzymes has been the focus of recent interest, but effective inhibitors have been difficult to identify. We describe a synthetic azetidine derivative, BRD4592, that kills Mycobacterium tuberculosis (Mtb) through allosteric inhibition of tryptophan synthase (TrpAB), a previously untargeted, highly allosterically regulated enzyme. BRD4592 binds at the TrpAB α-β-subunit interface and affects multiple steps in the enzyme's overall reaction, resulting in inhibition not easily overcome by changes in metabolic environment. We show that TrpAB is required for the survival of Mtb and Mycobacterium marinum in vivo and that this requirement may be independent of an adaptive immune response. This work highlights the effectiveness of allosteric inhibition for targeting proteins that are naturally highly dynamic and that are essential in vivo, despite their apparent dispensability under in vitro conditions, and suggests a framework for the discovery of a next generation of allosteric inhibitors.


    Organizational Affiliation

    The Broad Institute, Cambridge, Massachusetts, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tryptophan synthase alpha chain
A, G, E, C
276Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Gene Names: trpA
EC: 4.2.1.20
Find proteins for P9WFY1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WFY1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tryptophan synthase beta chain
B, H, F, D
410Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Gene Names: trpB
EC: 4.2.1.20
Find proteins for P9WFX9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WFX9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B, H
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
MLI
Query on MLI

Download SDF File 
Download CCD File 
A, C, E, G
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
B, D, F, H
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 135.137α = 90.00
b = 157.989β = 90.00
c = 166.651γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-3000data scaling
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of HealthUnited StatesHHSN272201200026C
Structure-guided Drug Discovery CoalitionCanada--

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence
  • Version 1.2: 2017-10-25
    Type: Database references