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 
  • R-Value Observed: 0.150 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1073/pnas.1703019114
  • Primary Citation of Related Structures:  
    5T4J, 5T4K, 5T4L

  • 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) 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate aminotransferase396Escherichia coliMutation(s): 0 
EC: 2.6.1.1
UniProt
Find proteins for P00509 (Escherichia coli (strain K12))
Explore P00509 
Go to UniProtKB:  P00509
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00509
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
77E
Query on 77E

Download Ideal Coordinates CCD File 
B [auth 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.913α = 90
b = 154.916β = 90
c = 79.342γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R15GM113229-01

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references
  • Version 1.2: 2017-04-19
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Advisory, Data collection, Database references, Refinement description