A large group of biosynthetic enzymes are able to catalyze the removal of the
ammonia group from glutamine and then to transfer this group to a substrate to
form a new carbon-nitrogen group. This catalytic activity is known as
glutamine amidotransferase (GATase) (EC 2.4.2.-) . The GATase domain exists
either as a separate polypeptidic subunit or as part of a larger polypeptide
fused in different ways to a synthase domain. On the basis of sequence
similarities two classes of GATase domains have been identified [2,3]: class-I
(also known as trpG-type or triad) (see <PDOC00405>) and class-II (also known
as purF-type or Ntn). Class-II (or type 2) GATase domains have been found in
the following enzymes:
Amido phosphoribosyltransferase (glutamine phosphoribosylpyrophosphate
amidotransferase) (EC 18.104.22.168). An enzyme which catalyzes the first step
in purine biosynthesis, the transfer of the ammonia group of glutamine to
PRPP to form 5-phosphoribosylamine (gene purF in bacteria, ADE4 in yeast).
Glucosamine--fructose-6-phosphate aminotransferase (EC 22.214.171.124). This
enzyme catalyzes a key reaction in amino sugar synthesis, the formation of
glucosamine 6-phosphate from fructose 6-phosphate and glutamine (gene glmS
in Escherichia coli, nodM in Rhizobium, GFA1 in yeast).
Asparagine synthetase (glutamine-hydrolyzing) (EC 126.96.36.199). This enzyme is
responsible for the synthesis of asparagine from aspartate and glutamine.
Glutamate synthase (gltS), an enzyme which participates in the ammonia
assimilation process by catalyzing the formation of glutamate from
glutamine and 2-oxoglutarate. Glutamate synthase is a multicomponent
iron-sulfur flavoprotein and three types occur which use a different
electron donor: NADPH-dependent gltS (large chain) (EC 188.8.131.52),
ferredoxin-dependent gltS (EC 184.108.40.206) and NADH-dependent gltS (EC
The active site is formed by a cysteine present at the N-terminal extremity of
the mature form of all these enzymes [5,6,7,8]. Two other conserved residues, Asn
and Gly, form an oxyanion hole for stabilization of the formed tetrahedral
intermediate. An insert of ~120 residues can occur between the conserved
regions . In some class-II GATases (for example in Bacillus subtilis or
chicken amido phosphoribosyltransferase) the enzyme is synthesized with a
short propeptide which is cleaved off post-translationally by a proposed
autocatalytic mechanism. Nuclear-encoded Fd-dependent gltS have a longer
propeptide which may contain a chloroplast-targeting peptide in additon to the
propeptide that is excised on enzyme activation .
The 3-D structure of the GATase type 2 domain forms a four layer
α/β/β/α architecture (see <PDB:1LM1>) which consists of a fold
similar to the N-terminal nucleophile (Ntn) hydrolases. These have the
capacity for nucleophilic attack and the possibility of autocatalytic
processing. The N-terminal position and the folding of the catalytic Cys
differ strongly from the Cys-His-Glu triad which forms the active site of
GATases of type 1 (see <PDOC00405>).
The profile we developed covers the entire GATase type 2 domain.
November 2006 / Pattern removed, profile added and text revised.
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