4TV7

Crystal structure of Bacillus subtilis GabR at 2.05 Angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Role of the aminotransferase domain in Bacillus subtilis GabR, a pyridoxal 5'-phosphate-dependent transcriptional regulator

Okuda, K.Kato, S.Ito, T.Shiraki, S.Kawase, Y.Goto, M.Kawashima, S.Hemmi, H.Fukada, H.Yoshimura, T.

(2015) Mol Microbiol 95: 245-257

  • DOI: 10.1111/mmi.12861
  • Primary Citation of Related Structures:  
    4TV7

  • PubMed Abstract: 
  • MocR/GabR family proteins are widely distributed prokaryotic transcriptional regulators containing pyridoxal 5'-phosphate (PLP), a coenzyme form of vitamin B6. The Bacillus subtilis GabR, probably the most extensively studied MocR/GabR family protein ...

    MocR/GabR family proteins are widely distributed prokaryotic transcriptional regulators containing pyridoxal 5'-phosphate (PLP), a coenzyme form of vitamin B6. The Bacillus subtilis GabR, probably the most extensively studied MocR/GabR family protein, consists of an N-terminal DNA-binding domain and a PLP-binding C-terminal domain that has a structure homologous to aminotransferases. GabR suppresses transcription of gabR and activates transcription of gabT and gabD, which encode γ-aminobutyrate (GΑΒΑ) aminotransferase and succinate semialdehyde dehydrogenase, respectively, in the presence of PLP and GABA. In this study, we examined the mechanism underlying GabR-mediated gabTD transcription with spectroscopic, crystallographic and thermodynamic studies, focusing on the function of the aminotransferase domain. Spectroscopic studies revealed that GABA forms an external aldimine with the PLP in the aminotransferase domain. Isothermal calorimetry demonstrated that two GabR molecules bind to the 51-bp DNA fragment that contains the GabR-binding region. GABA minimally affected ΔG(binding) upon binding of GabR to the DNA fragment but greatly affected the contributions of ΔH and ΔS to ΔG(binding). GABA forms an external aldimine with PLP and causes a conformational change in the aminotransferase domain, and this change likely rearranges GabR binding to the promoter and thus activates gabTD transcription.


    Organizational Affiliation

    Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Frou-chou, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HTH-type transcriptional regulatory protein GabRABCD479Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: gabRycnFBSU03890
Find proteins for P94426 (Bacillus subtilis (strain 168))
Explore P94426 
Go to UniProtKB:  P94426
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
A,B,C,DL-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.831α = 90
b = 101.556β = 90
c = 212.987γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SOLVEphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
RESOLVEmodel building
REFMACrefinement
SOLVEmodel building
REFMAC5refinement
HKLdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2017-03-15
    Changes: Database references
  • Version 1.2: 2020-01-29
    Changes: Data collection