5T4J

PLP and GABA Trigger GabR-Mediated Transcription Regulation in Bacillus subsidies via External Aldimine Formation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.231 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

PLP and GABA trigger GabR-mediated transcription regulation in Bacillus subtilis via external aldimine formation.

Wu, R.Sanishvili, R.Belitsky, B.R.Juncosa, J.I.Le, H.V.Lehrer, H.J.Farley, M.Silverman, R.B.Petsko, G.A.Ringe, D.Liu, D.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: 3891-3896

  • DOI: 10.1073/pnas.1703019114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Bacillus subtilis protein regulator of the gabTD operon and its own gene (GabR) is a transcriptional activator that regulates transcription of γ-aminobutyric acid aminotransferase (GABA-AT; GabT) upon interactions with pyridoxal-5'-phosphate (PLP ...

    The Bacillus subtilis protein regulator of the gabTD operon and its own gene (GabR) is a transcriptional activator that regulates transcription of γ-aminobutyric acid aminotransferase (GABA-AT; GabT) upon interactions with pyridoxal-5'-phosphate (PLP) and GABA, and thereby promotes the biosynthesis of glutamate from GABA. We show here that the external aldimine formed between PLP and GABA is apparently responsible for triggering the GabR-mediated transcription activation. Details of the "active site" in the structure of the GabR effector-binding/oligomerization (Eb/O) domain suggest that binding a monocarboxylic γ-amino acid such as GABA should be preferred over dicarboxylic acid ligands. A reactive GABA analog, (S)-4-amino-5-fluoropentanoic acid (AFPA), was used as a molecular probe to examine the reactivity of PLP in both GabR and a homologous aspartate aminotransferase (Asp-AT) from Escherichia coli as a control. A comparison between the structures of the Eb/O-PLP-AFPA complex and Asp-AT-PLP-AFPA complex revealed that GabR is incapable of facilitating further steps of the transamination reaction after the formation of the external aldimine. Results of in vitro and in vivo assays using full-length GabR support the conclusion that AFPA is an agonistic ligand capable of triggering GabR-mediated transcription activation via formation of an external aldimine with PLP.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HTH-type transcriptional regulatory protein GabR
B
365Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: gabR (ycnF)
Find proteins for P94426 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P94426
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ABU
Query on ABU

Download SDF File 
Download CCD File 
B
GAMMA-AMINO-BUTANOIC ACID
GAMMA(AMINO)-BUTYRIC ACID
C4 H9 N O2
BTCSSZJGUNDROE-UHFFFAOYSA-N
 Ligand Interaction
PLP
Query on PLP

Download SDF File 
Download CCD File 
B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.231 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.172 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 92.364α = 90.00
b = 128.894β = 90.00
c = 65.096γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States1R15GM113229-01

Revision History 

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-04-12
    Type: Database references
  • Version 1.2: 2017-04-26
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence