5T4L

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.149 

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 <i>Bacillus subtilis </i> protein regulator of the <i>gabTD </i> 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 ...

    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, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, IL 60208-3113.,Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY 10065.,Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454.,Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660.,Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454; dliu@luc.edu gpetsko@med.cornell.edu.,Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111.,Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL 60660; dliu@luc.edu gpetsko@med.cornell.edu.,GM/CA@APS, The X-Ray Science Division, the Advanced Photon Source, Argonne National Laboratory, Lemont, IL 60439.,Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston, IL 60208-3113.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate aminotransferase
A
396Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: aspC
EC: 2.6.1.1
Find proteins for P00509 (Escherichia coli (strain K12))
Go to UniProtKB:  P00509
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
77E
Query on 77E

Download SDF File 
Download CCD File 
A
(4R)-4-amino-6-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}hexanoic acid
C13 H21 N2 O7 P
CFDRNBOOPNTUHH-SNVBAGLBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.149 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 84.913α = 90.00
b = 154.916β = 90.00
c = 79.342γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

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: 2017-04-19
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence