6J2V

GABA aminotransferase from Corynebacterium glutamicum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of gamma-aminobutyrate aminotransferase in complex with a PLP-GABA adduct from Corynebacterium glutamicum.

Hong, J.Kim, K.J.

(2019) Biochem Biophys Res Commun 514: 601-606

  • DOI: https://doi.org/10.1016/j.bbrc.2019.04.194
  • Primary Citation of Related Structures:  
    6J2V

  • PubMed Abstract: 

    γ-Aminobutyrate (GABA), a four carbon non-protein amino acid, is used by some microorganisms as a source of carbon and/or nitrogen. Corynebacterium glutamicum has an incomplete GABA shunt that lacks a glutamate decarboxylase coding gene for the conversion of glutamate to GABA. Recently, a novel GABA assimilation system was identified in C. glutamicum. In the cell, GABA aminotransferase (GABA-AT) is the first step of GABA assimilation in the process of utilizing GABA as a carbon and/or nitrogen source. In this study, we report the crystal structure of CgGABA-AT in complex with PLP-GABA. We used structural studies and site-directed mutagenesis experiments to identify the key residues that contribute to the formation of the active site. Furthermore, based on structural comparisons and amino acid sequence alignment, we demonstrate the differences between the GABA-ATs of bacteria, fungi, and animals.


  • Organizational Affiliation

    School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PLP-dependent aminotransferases
A, B, C, D
473Corynebacterium glutamicum ATCC 13032Mutation(s): 0 
Gene Names: Cgl0479
EC: 2.6.1.19
UniProt
Find proteins for Q8NT35 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534))
Explore Q8NT35 
Go to UniProtKB:  Q8NT35
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NT35
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLZ
Query on PLZ

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
K [auth C],
O [auth D]
4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]BUTANOIC ACID
C12 H19 N2 O7 P
DOHWOHSLOVXAFH-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth B]
J [auth B]
L [auth C]
F [auth A],
G [auth A],
H [auth B],
J [auth B],
L [auth C],
M [auth C],
N [auth D],
P [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.148 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.725α = 106.57
b = 70.495β = 96.48
c = 97.017γ = 110.66
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references