7X4Y

Crystal structure of Bacteroides thetaiotaomicron glutamate decarboxylase BTGAD-PLP-GABA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Coordinated regulation of Bacteroides thetaiotaomicron glutamate decarboxylase activity by multiple elements under different pH.

Liu, S.Wen, B.Du, G.Wang, Y.Ma, X.Yu, H.Zhang, J.Fan, S.Zhou, H.Xin, F.

(2023) Food Chem 403: 134436-134436

  • DOI: https://doi.org/10.1016/j.foodchem.2022.134436
  • Primary Citation of Related Structures:  
    7X4L, 7X4Y, 7X51, 7X52

  • PubMed Abstract: 

    Glutamate decarboxylase catalyzes the conversion of glutamate to γ-aminobutyric acid, which plays a vital role in the gut-brain axis. Herein, a novel glutamate decarboxylase from Bacteroides thetaiotaomicron (BTGAD) was heterologously expressed. BTGAD possessed high catalytic efficiency at 60℃ and pH 3.6. As pH response, N-terminal sequence (NTS), C-terminal sequence (CTS), and β-hairpin in BTGAD coordinately regulated its activity under different pH. NTS folded into a loop under acidic pH, and the truncation of NTS severely reduced its activity to 4.2%. While CTS occupied the active site under neutral pH and became disordered to release the inhibition effect under acidic conditions. The β-hairpin, located near the active site, swung and formed open and closed conformations, which acted as an activity switch. This study provides the molecular basis for the coordinated regulation mechanism of BTGAD and lays a theoretical foundation for understanding the metabolism of dietary glutamate and its interaction relationships with the gut-brain axis.


  • Organizational Affiliation

    Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate decarboxylase
A, B, C, D, E
A, B, C, D, E, F
481Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT_2570
EC: 4.1.1.15
UniProt
Find proteins for Q8A4M9 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A4M9 
Go to UniProtKB:  Q8A4M9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A4M9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth D]
O [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth D],
O [auth E],
Q [auth F]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
ABU (Subject of Investigation/LOI)
Query on ABU

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
GAMMA-AMINO-BUTANOIC ACID
C4 H9 N O2
BTCSSZJGUNDROE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.736α = 90
b = 130.689β = 100.04
c = 109.761γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChinaS2020JBKY-13

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Structure summary
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection
  • Version 2.1: 2023-11-29
    Changes: Refinement description