4ZSW

Pig Brain GABA-AT inactivated by (E)-(1S,3S)-3-Amino-4-fluoromethylenyl-1-cyclopentanoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of Inactivation of GABA Aminotransferase by (E)- and (Z)-(1S,3S)-3-Amino-4-fluoromethylenyl-1-cyclopentanoic Acid.

Lee, H.Le, H.V.Wu, R.Doud, E.Sanishvili, R.Kellie, J.F.Compton, P.D.Pachaiyappan, B.Liu, D.Kelleher, N.L.Silverman, R.B.

(2015) Acs Chem.Biol. 10: 2087-2098

  • DOI: 10.1021/acschembio.5b00212
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • When γ-aminobutyric acid (GABA), the major inhibitory neurotransmitter in the mammalian central nervous system, falls below a threshold level, seizures occur. One approach to raise GABA concentrations is to inhibit GABA aminotransferase (GABA-AT), a ...

    When γ-aminobutyric acid (GABA), the major inhibitory neurotransmitter in the mammalian central nervous system, falls below a threshold level, seizures occur. One approach to raise GABA concentrations is to inhibit GABA aminotransferase (GABA-AT), a pyridoxal 5'-phosphate-dependent enzyme that degrades GABA. We have previously developed (1S,3S)-3-amino-4-difluoromethylene-1-cyclopentanoic acid (CPP-115), which is 186 times more efficient in inactivating GABA-AT than vigabatrin, the only FDA-approved inactivator of GABA-AT. We also developed (E)- and (Z)-(1S,3S)-3-amino-4-fluoromethylenyl-1-cyclopentanoic acid (1 and 2, respectively), monofluorinated analogs of CPP-115, which are comparable to vigabatrin in inactivating GABA-AT. Here, we report the mechanism of inactivation of GABA-AT by 1 and 2. Both produce a metabolite that induces disruption of the Glu270-Arg445 salt bridge to accommodate interaction between the metabolite formyl group and Arg445. This is the second time that Arg445 has interacted with a ligand and is involved in GABA-AT inactivation, thereby confirming the importance of Arg445 in future inactivator design.


    Organizational Affiliation

    Departments of Chemistry and Molecular Biosciences, Chemistry of Life Processes Institute, and the Center for Molecular Innovation and Drug Discovery, Northwestern University , Evanston, Illinois 60208, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-aminobutyrate aminotransferase, mitochondrial
A, B, C, D
461Sus scrofaMutation(s): 0 
Gene Names: ABAT (GABAT)
EC: 2.6.1.19
Find proteins for P80147 (Sus scrofa)
Go to Gene View: ABAT
Go to UniProtKB:  P80147
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FSF
Query on FSF

Download SDF File 
Download CCD File 
A, C
4FE-2S-O HYBRID CLUSTER
Fe4 O S2
ANJSROJJSKUDEH-RDKWERHRAJ
 Ligand Interaction
RW2
Query on RW2

Download SDF File 
Download CCD File 
A, B, C, D
(1S)-4-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]cyclopent-3-ene-1,3-dicarboxylic acid
C15 H19 N2 O9 P
VNQKGJPXVHNUEY-QMMMGPOBSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.601α = 90.00
b = 227.614β = 108.97
c = 71.343γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM066132
National Institutes of Health/National Institute on Drug AbuseUnited StatesDA030604
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM067725
National Institutes of HealthUnited StatesACB-12002
National Institutes of Health/National Institute of General Medical SciencesUnited StatesAGM-12006
Department of Energy (United States)United StatesDE-AC02-06CH11357

Revision History 

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2015-09-30
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Advisory, Author supporting evidence, Derived calculations