5GP4

Lactobacillus brevis CGMCC 1306 Glutamate decarboxylase

  • Classification: LYASE
  • Organism(s): Levilactobacillus brevis
  • Expression System: Escherichia coli BL21
  • Mutation(s): No 

  • Deposited: 2016-07-31 Released: 2017-08-02 
  • Deposition Author(s): Mei, L., Huang, J.
  • Funding Organization(s): National Natural Science Foundation of China, the Natural Science Foundation of Zhejiang Province

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


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Literature

Lactobacillus brevis CGMCC 1306 glutamate decarboxylase: Crystal structure and functional analysis.

Huang, J.Fang, H.Gai, Z.C.Mei, J.Q.Li, J.N.Hu, S.Lv, C.J.Zhao, W.R.Mei, L.H.

(2018) Biochem Biophys Res Commun 503: 1703-1709

  • DOI: 10.1016/j.bbrc.2018.07.102
  • Primary Citation of Related Structures:  
    5GP4

  • PubMed Abstract: 
  • Glutamate decarboxylase (GAD), which is a unique pyridoxal 5-phosphate (PLP)-dependent enzyme, can catalyze α-decarboxylation of l-glutamate (L-Glu) to γ-aminobutyrate (GABA). The crystal structure of GAD in complex with PLP from Lactobacillus brevis CGMCC 1306 was successfully solved by molecular-replacement, and refined at 2 ...

    Glutamate decarboxylase (GAD), which is a unique pyridoxal 5-phosphate (PLP)-dependent enzyme, can catalyze α-decarboxylation of l-glutamate (L-Glu) to γ-aminobutyrate (GABA). The crystal structure of GAD in complex with PLP from Lactobacillus brevis CGMCC 1306 was successfully solved by molecular-replacement, and refined at 2.2 Å resolution to an R work factor of 18.76% (R free  = 23.08%). The coenzyme pyridoxal 5-phosphate (PLP) forms a Schiff base with the active-site residue Lys279 by continuous electron density map, which is critical for catalysis by PLP-dependent decarboxylase. Gel filtration showed that the active (pH 4.8) and inactive (pH 7.0) forms of GAD are all dimer. The residues (Ser126, Ser127, Cys168, Ile211, Ser276, His278 and Ser321) play important roles in anchoring PLP cofactor inside the active site and supporting its catalytic reactivity. The mutant T215A around the putative substrate pocket displayed an 1.6-fold improvement in catalytic efficiency (k cat /K m ) compared to the wild-type enzyme (1.227 mM -1  S -1 versus 0.777 mM -1  S -1 ), which was the highest activity among all variants tested. The flexible loop (Tyr308-Glu312), which is positioned near the substrate-binding site, is involved in the catalytic reaction, and the conserved residue Tyr308 plays a vital role in decarboxylation of L-Glu.


    Organizational Affiliation

    Department of Biological and Pharmaceutical Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo, 315100, PR China. Electronic address: meilh@zju.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate decarboxylaseB [auth A],
C [auth B],
A [auth C]
468Levilactobacillus brevisMutation(s): 0 
Gene Names: gad
EC: 4.1.1.15
UniProt
Find proteins for D6PXK5 (Levilactobacillus brevis)
Explore D6PXK5 
Go to UniProtKB:  D6PXK5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6PXK5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
D [auth C],
E [auth A],
F [auth B]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.333α = 90
b = 170.129β = 90
c = 164.567γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data collection
SCALEPACKdata scaling
PHASERphasing
MERLOTdata processing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-07-31 
  • Released Date: 2017-08-02 
  • Deposition Author(s): Mei, L., Huang, J.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina21176220 and 31470793
the Natural Science Foundation of Zhejiang ProvinceChinaZ13B060008 and LY16B060008

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2018-09-12
    Changes: Data collection, Database references