5X03

Crystal structure of the C-terminal domain of Bacillus subtilis GabR reveals a closed conformation by the binding of gamma-aminobutyric acid, inducing the transcriptional activation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal structure of the C-terminal domain of Bacillus subtilis GabR reveals a closed conformation by gamma-aminobutyric acid binding, inducing transcriptional activation

Park, S.A.Park, Y.S.Lee, K.S.

(2017) Biochem Biophys Res Commun 487: 287-291

  • DOI: 10.1016/j.bbrc.2017.04.052
  • Primary Citation of Related Structures:  
    5X03

  • PubMed Abstract: 
  • Bacillus subtilis GabR (BsGabR) is involved in the γ-aminobutyric acid (GABA) catabolism as a transcriptional regulator, consisting of an N-terminal helix-turn-helix DNA-binding domain and a C-terminal aminotransferase-like (AT-like) domain. Research on the C-terminal AT-like domain of BsGabR (BsGabR-CTD) has focused on the interaction with GABA as an effector, but most its functional details remain unclear ...

    Bacillus subtilis GabR (BsGabR) is involved in the γ-aminobutyric acid (GABA) catabolism as a transcriptional regulator, consisting of an N-terminal helix-turn-helix DNA-binding domain and a C-terminal aminotransferase-like (AT-like) domain. Research on the C-terminal AT-like domain of BsGabR (BsGabR-CTD) has focused on the interaction with GABA as an effector, but most its functional details remain unclear. To understand the underlying mechanism, we report the crystal structure of BsGabR-CTD in complex with pyridoxal 5'-phosphate (PLP) and GABA at 2.0 Å resolution. The structure of ligand-bound BsGabR-CTD revealed two distinct monomeric states in a homodimer. One subunit is a closed-form containing the PLP-GABA adduct, and the other subunit is a PLP-bound open-form. Our structural studies provide a detailed mechanism indicating that the open-to-closed transition by the binding of GABA induces the conformational rearrangement of BsGabR-CTD, which may trigger the activation of transcription.


    Organizational Affiliation

    Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan 46252, Republic of Korea. Electronic address: kslee@cup.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HTH-type transcriptional regulatory protein GabRA363Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: gabRycnFBSU03890
UniProt
Find proteins for P94426 (Bacillus subtilis (strain 168))
Explore P94426 
Go to UniProtKB:  P94426
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HTH-type transcriptional regulatory protein GabRB365Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
Gene Names: gabRycnFBSU03890
UniProt
Find proteins for P94426 (Bacillus subtilis (strain 168))
Explore P94426 
Go to UniProtKB:  P94426
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
ABU
Query on ABU

Download Ideal Coordinates CCD File 
D [auth A]GAMMA-AMINO-BUTANOIC ACID
C4 H9 N O2
BTCSSZJGUNDROE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.497α = 90
b = 118.497β = 90
c = 75.862γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2017-01-19 
  • Released Date: 2017-05-24 
  • Deposition Author(s): Park, S.A., Lee, K.S.

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release