5TCI

Crystal structure of tryptophan synthase from M. tuberculosis - BRD4592-bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.3 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, 5TCF, 5TCI, 5TCH, 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

    Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophan synthase alpha chainACEG276Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: trpARv1613MTCY01B2.05
EC: 4.2.1.20
Find proteins for P9WFY1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFY1 
Go to UniProtKB:  P9WFY1
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophan synthase beta chainBDFH410Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: trpBRv1612MTCY01B2.04
EC: 4.2.1.20
Find proteins for P9WFX9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFX9 
Go to UniProtKB:  P9WFX9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
79V
Query on 79V

Download CCD File 
B, D, F, H
(2R,3S,4R)-3-(2'-fluoro[1,1'-biphenyl]-4-yl)-4-(hydroxymethyl)azetidine-2-carbonitrile
C17 H15 F N2 O
RECLLIAWOQFAMC-ULQDDVLXSA-N
 Ligand Interaction
MLI
Query on MLI

Download CCD File 
A, C, E, G
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
FMT
Query on FMT

Download CCD File 
A, B, C, D, F, G, H
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
B,D,F,HL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
79VIC50:  22.600000381469727   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.955α = 90
b = 158.335β = 90
c = 166.631γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant 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: 2017-07-26
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence