(S)-4-Amino-5-phenoxypentanoate as a Selective Agonist of the Transcription Factor GabR

  • Classification: TRANSCRIPTION
  • Organism(s): Bacillus subtilis subsp. subtilis str. 168
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-11-09 Released: 2020-10-07 
  • Deposition Author(s): Catlin, D.S., Liu, D.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report

This is version 1.0 of the entry. See complete history


(S)-4-Amino-5-phenoxypentanoate designed as a potential selective agonist of the bacterial transcription factor GabR.

Catlin, D.S.Reidl, C.T.Trzupek, T.R.Silverman, R.B.Cannon, B.L.Becker, D.P.Liu, D.

(2020) Protein Sci 29: 1816-1828

  • DOI: https://doi.org/10.1002/pro.3905
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Addressing molecular recognition in the context of evolution requires pursuing new molecular targets to enable the development of agonists or antagonists with new mechanisms of action. Disruption of transcriptional regulation through targeting transcription factors that regulate the expression of key enzymes in bacterial metabolism may provide a promising method for controlling the bacterial metabolic pathways. To this end, we have selectively targeted a bacterial transcription regulator through the design and synthesis of a series of γ-aminobutyric acid (GABA) derivatives, including (S)-4-amino-5-phenoxypentanoate (4-phenoxymethyl-GABA), which are based on docking insights gained from a previously-solved crystal structure of GabR from Bacillus subtilis. This target was selected because GabR strictly controls GABA metabolism by regulating the transcription of the gabT/D operon. These GabR transcription modulators are selective for the bacterial transcription factor GabR and are unable to bind to structural homologs of GabR due to distinct steric constraints. We have obtained a crystal structure of 4-phenoxymethyl-GABA bound as an external aldimine with PLP in the effector binding site of GabR, which suggests that this compound is capable of binding and reacting in the same manner as the native effector ligand. Inhibition assays demonstrate high selectivity of 4-phenoxymethyl-GABA for bacterial GabR versus several selected eukaryotic enzymes. Single-molecule fluorescence resonance energy transfer (smFRET) experiments reveal a ligand-induced DNA distortion that is very similar to that of the native effector GABA, suggesting that the compound functions as a potential selective agonist of GabR.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HTH-type transcriptional regulatory protein GabRA [auth B],
B [auth C]
364Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: gabRycnFBSU03890
Find proteins for P94426 (Bacillus subtilis (strain 168))
Explore P94426 
Go to UniProtKB:  P94426
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP94426
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QL4 (Subject of Investigation/LOI)
Query on QL4

Download Ideal Coordinates CCD File 
F [auth B],
J [auth C]
(4S)-4-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-5-phenoxypentanoic acid
C19 H23 N2 O8 P
Query on SO4

Download Ideal Coordinates CCD File 
C [auth B]
D [auth B]
E [auth B]
G [auth C]
H [auth C]
C [auth B],
D [auth B],
E [auth B],
G [auth C],
H [auth C],
I [auth C]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.65α = 90
b = 152.65β = 90
c = 69.16γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
iMOSFLMdata reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR15GM113229
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesR01 DA030604
National Science Foundation (NSF, United States)United StatesECCS-1542205

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-07
    Type: Initial release