Glutamate synthase, eukaryotic (IPR012220)

Short name: Glu_synth_euk

Overlapping homologous superfamilies


Family relationships



This group represents the eukaryotic type of glutamate synthase (NADH-GOGAT, EC: This pyridine-linked form is found in both photosynthetic and nonphotosynthetic eukaryotes. It displays a single-subunit structure corresponding to the fusion of the small and the large bacterial subunits.

Glutamate synthase (GOGAT, GltS) is a complex iron-sulphur flavoprotein that catalyses the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the bacterial, yeast and plant pathways for ammonia assimilation [PMID: 11188694]. GOGAT is a multifunctional enzyme that functions through three distinct active centres carrying out multiple reaction steps: L-glutamine hydrolysis, conversion of 2-oxoglutarate into L-glutamate, and electron uptake from an electron donor [PMID: 11967268]. The small subunit functions as a FAD-dependent NADPH oxidoreductase, which serves to transfer reducing equivalents to the site of glutamate synthesis on the large subunit through the enzyme [3Fe-4S] cluster (on the large subunit) and at least one of its [4Fe-4S] centres [PMID: 10357231, PMID: 12455964]. The large subunit contains the GltS L-glutamine amidotransferase (GAT) site where L-Gln binds and is hydrolysed to yield L-Glu and ammonia. The latter is transferred through the intramolecular ammonia tunnel [PMID: 11188694] to the glutamate synthase site where 2-OG binds, is converted to the iminoglutarate (2-IG) intermediate, and reduced to L-Glu by receiving reducing equivalents from the reduced FMN cofactor at this site [PMID: 12069605].

There are four classes of GOGAT [PMID: 10357231, PMID: 11230537]:

1. Bacterial NADPH-dependent GOGAT (NADPH-GOGAT, EC: This standard bacterial NADPH-GOGAT is composed of a large (alpha, GltB) subunit and a small (beta, GltD) subunit.

2. Ferredoxin-dependent form in cyanobacteria and plants (Fd-GOGAT from photosynthetic cells, EC: displays a single-subunit structure corresponding to the large bacterial subunit.

3. Pyridine-linked form in both photosynthetic and nonphotosynthetic eukaryotes (eukaryotic GOGAT or NADH-GOGAT, EC: displays a single-subunit structure corresponding to the fusion of the small and the large bacterial subunits.

4. The archaeal type with stand-alone proteins corresponding to the N-terminal, FMN-binding, and the C-terminal domains of the large subunit [PMID: 11230537, PMID: 10357231] (IPR012375, IPR012061), and to the small subunit.

The large subunit of GOGAT consists of three domains: N-terminal domain (amidotransferase domain IPR017932); central (consisting of IPR006982 and the FMN-binding domain IPR002932), and the C-terminal domain (IPR002489).

The N-terminal amidotransferase domain is characterised by a four layer alpha/beta/beta/alpha architecture and is similar to other Ntn-amidotransferases [PMID: 11967268]. It contains the typical catalytic centre of Ntn-amidotransferases, and the N-terminal Cys-1 catalyses the hydrolysis of L-glutamine generating ammonia and the first molecule of L-glutamate [PMID: 11967268].

The second (central) domain consists of IPR006982 and IPR002932. IPR006982 connects the amidotransferase domain with the FMN-binding domain and has an alpha/beta overall topology [PMID: 11967268]. The FMN-binding domain (IPR002932) has a classic beta/alpha barrel topology. In this domain, the 2-iminoglutarate intermediate, formed upon the addition of ammonia onto 2-oxoglutarate, is reduced by the FMN cofactor producing the second molecule of L-glutamate [PMID: 11967268]. This domain also contains the enzyme 3Fe-4S cluster [PMID: 11967268].

The C-terminal, or GXGXG structural domain, has a right-handed beta-helix topology composing seven beta-helical turns. This domain does not have a direct function in glutamate synthase activity but rather a structural function through extensive interactions with the amidotransferase and FMN-binding domains [PMID: 11188694, PMID: 11967268].

The structural data combined with the catalytic properties of GltS indicate that binding of ferredoxin and 2-oxoglutarate to the FMN-binding domain of GltS induce a conformational change in the loop connecting the two catalytic centres. The rearrangement induces a shift in the catalytic elements of the amidotransferase domain, such that it becomes activated [PMID: 11967268].

For additional information please see [PMID: 7836314].

GO terms

Biological Process

GO:0006537 glutamate biosynthetic process

Molecular Function

GO:0010181 FMN binding
GO:0050660 flavin adenine dinucleotide binding
GO:0016040 glutamate synthase (NADH) activity
GO:0005506 iron ion binding

Cellular Component

No terms assigned in this category.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.