PDBsum entry 1ohy

Transferase

PDB id: 1ohy

Contents

Protein chains

461 a.a. *

Ligands

PLP-GEG ×4

FES ×2

Waters ×284

* Residue conservation analysis

PDB id:

1ohy

Name:

Transferase

Title:

4-aminobutyrate-aminotransferase inactivated by gamma-ethynyl gaba

Structure:

4-aminobutyrate aminotransferase. Chain: a, b, c, d. Synonym: mitochondrial precursor, gamma-amino-n-butyrate transaminase, gaba transaminase, gaba aminotransferase, gaba-at, gaba-t, abat, gabat. Other_details: after reaction with 4-amino-5-hexynoic acid (geg) (gamma-ethynyl gaba) the fragment geg has been generated which is covalently attached via a double bond to c4a of plp and via a single bond to nz of the active site lys 329

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Organ: liver

Biol. unit:

Dimer (from PDB file)

Resolution:

2.80Å R-factor: 0.198 R-free: 0.229

Authors:

P.Storici,T.Schirmer

Key ref:

P.Storici et al. (2004). Structures of gamma-aminobutyric acid (GABA) aminotransferase, a pyridoxal 5'-phosphate, and [2Fe-2S] cluster-containing enzyme, complexed with gamma-ethynyl-GABA and with the antiepilepsy drug vigabatrin. J Biol Chem, 279, 363-373. PubMed id: 14534310 DOI: 10.1074/jbc.M305884200

Date:

03-Jun-03 Release date: 16-Oct-03

Protein chains

P80147  (GABT_PIG) -  4-aminobutyrate aminotransferase, mitochondrial from Sus scrofa

Seq: 500 a.a.

Struc: 461 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.6.1.19 - 4-aminobutyrate--2-oxoglutarate transaminase.
• Reaction: 4-aminobutanoate + 2-oxoglutarate = succinate semialdehyde + L-glutamate

4-aminobutanoate (Bound ligand (Het Group name = GEG) matches with 77.78% similarity) + 2-oxoglutarate = succinate semialdehyde + L-glutamate

• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

• Enzyme class 2: E.C.2.6.1.22 - (S)-3-amino-2-methylpropionate transaminase.

Pathway:

• Reaction: (S)-3-amino-2-methylpropanoate + 2-oxoglutarate = 2-methyl-3- oxopropanoate + L-glutamate

(S)-3-amino-2-methylpropanoate + 2-oxoglutarate = 2-methyl-3- oxopropanoate + L-glutamate (Bound ligand (Het Group name = GEG) matches with 72.73% similarity)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M305884200

J Biol Chem 279:363-373 (2004)

PubMed id: 14534310

Structures of gamma-aminobutyric acid (GABA) aminotransferase, a pyridoxal 5'-phosphate, and [2Fe-2S] cluster-containing enzyme, complexed with gamma-ethynyl-GABA and with the antiepilepsy drug vigabatrin.

P.Storici, D.De Biase, F.Bossa, S.Bruno, A.Mozzarelli, C.Peneff, R.B.Silverman, T.Schirmer.

ABSTRACT

Gamma-aminobutyric acid aminotransferase (GABA-AT) is a pyridoxal 5'-phosphate-dependent enzyme responsible for the degradation of the inhibitory neurotransmitter GABA. GABA-AT is a validated target for antiepilepsy drugs because its selective inhibition raises GABA concentrations in brain. The antiepilepsy drug, gamma-vinyl-GABA (vigabatrin) has been investigated in the past by various biochemical methods and resulted in several proposals for its mechanisms of inactivation. In this study we solved and compared the crystal structures of pig liver GABA-AT in its native form (to 2.3-A resolution) and in complex with vigabatrin as well as with the close analogue gamma-ethynyl-GABA (to 2.3 and 2.8 A, respectively). Both inactivators form a covalent ternary adduct with the active site Lys-329 and the pyridoxal 5'-phosphate (PLP) cofactor. The crystal structures provide direct support for specific inactivation mechanisms proposed earlier on the basis of radio-labeling experiments. The reactivity of GABA-AT crystals with the two GABA analogues was also investigated by polarized absorption microspectrophotometry. The spectral data are discussed in relation to the proposed mechanism. Intriguingly, all cluster of yet unknown function at the center of the dimeric molecule in the vicinity of the PLP cofactors.

Selected figure(s)

Figure 1.
FIG. 1. Stereographic projection of the active site of GABA-AT. The final model is shown together with the 2F[o] - F[c] map (contour level, 1.2 ). An acetate molecule is found close to Arg-192, i.e. at a position where the carboxylate moiety of the natural substrate GABA is expected to bind (6).

Figure 3.
FIG. 3. The [2Fe-2S] cluster at the center of the GABA-AT dimer. A, structure of the GABA-AT dimer. The view is approximately along the molecular 2-fold symmetry axis. The C traces of the two subunits are shown in black and red. Helix 5 and its symmetry mate are highlighted by thick gray traces. The [2Fe-2S] cluster on the molecular 2-fold symmetry axis together with the liganding cysteines and the two symmetry related PLP cofactors are shown in full view. B, close-up view of A. The C traces have been omitted for clarity. Symmetry-related residues are marked with the symbol "#." C, stereographic close-up view. The molecular 2-fold axis is approximately along the vertical direction. The native 2F[o] - F[c] omit map (magenta; contour level 1.2 ) and the anomalous difference map (light blue; contour level 4.5 ) were computed with data to 2.3-Å resolution (data set of the vigabatrin complex). The iron and sulfur atoms were not included for phasing.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 363-373) copyright 2004.

Figures were selected by an automated process.