Phosphoribosylamine—glycine ligase, also known as glycinamide ribonucleotide synthetase (GARS), () is an
enzyme
An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...
that
catalyzes
Catalysis () is the increase in rate of a chemical reaction due to an added substance known as a catalyst (). Catalysts are not consumed by the reaction and remain unchanged after it. If the reaction is rapid and the catalyst recycles quick ...
the
chemical reaction
A chemical reaction is a process that leads to the chemistry, chemical transformation of one set of chemical substances to another. When chemical reactions occur, the atoms are rearranged and the reaction is accompanied by an Gibbs free energy, ...
:ATP + 5-phospho-
D-ribosylamine + glycine
ADP + phosphate +
which is the second step in
purine biosynthesis
Purine metabolism refers to the metabolic pathways to synthesize and break down purines that are present in many organisms.
Biosynthesis
Purines are biologically synthesized as nucleotides and in particular as ribotides, i.e. bases attached to ...
.
The 3
substrates of this enzyme are
ATP,
5-phospho-D-ribosylamine, and
glycine
Glycine (symbol Gly or G; ) is an amino acid that has a single hydrogen atom as its side chain. It is the simplest stable amino acid. Glycine is one of the proteinogenic amino acids. It is encoded by all the codons starting with GG (G ...
, whereas its 3
products
Product may refer to:
Business
* Product (business), an item that can be offered to a market to satisfy the desire or need of a customer.
* Product (project management), a deliverable or set of deliverables that contribute to a business solution
...
are
ADP,
phosphate
Phosphates are the naturally occurring form of the element phosphorus.
In chemistry, a phosphate is an anion, salt, functional group or ester derived from a phosphoric acid. It most commonly means orthophosphate, a derivative of orthop ...
, and .
This enzyme belongs to the family of
ligase
In biochemistry, a ligase is an enzyme that can catalyze the joining ( ligation) of two molecules by forming a new chemical bond. This is typically via hydrolysis of a small pendant chemical group on one of the molecules, typically resulting i ...
s, specifically those forming generic carbon-nitrogen bonds.
In
bacteria
Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...
, GARS is a monofunctional
enzyme
An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...
(encoded by the purD gene). The purD genes often contain
PurD RNA motif in their
5' UTR
The 5′ untranslated region (also known as 5′ UTR, leader sequence, transcript leader, or leader RNA) is the region of a messenger RNA (mRNA) that is directly Upstream and downstream (DNA), upstream from the initiation codon. This region is im ...
.
In
yeast
Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom (biology), kingdom. The first yeast originated hundreds of millions of years ago, and at least 1,500 species are currently recognized. They are est ...
, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with
phosphoribosylformylglycinamidine cyclo-ligase (AIRS). In higher
eukaryotes
The eukaryotes ( ) constitute the domain of Eukaryota or Eukarya, organisms whose cells have a membrane-bound nucleus. All animals, plants, fungi, seaweeds, and many unicellular organisms are eukaryotes. They constitute a major group of ...
, including humans,
GARS is part of a trifunctional enzyme in conjunction with AIRS and with
phosphoribosylglycinamide formyltransferase
Phosphoribosylglycinamide formyltransferase (), also known as glycinamide ribonucleotide transformylase (GAR Tfase), is an enzyme with systematic name ''10-formyltetrahydrofolate:5'-phosphoribosylglycinamide N-formyltransferase''. This enzyme cat ...
(GART),
forming
GARS-AIRS-GART.
Nomenclature
The
systematic name
A systematic name is a name given in a systematic way to one unique group, organism, object or chemical substance, out of a specific population or collection. Systematic names are usually part of a nomenclature.
A semisystematic name or semitrivi ...
of this enzyme class is 5-phospho-D-ribosylamine:glycine ligase (ADP-forming). Other names in common use include:
* phosphoribosylglycinamide synthetase
* glycinamide ribonucleotide synthetase
* phosphoribosylglycineamide synthetase
* glycineamide ribonucleotide synthetase
* 2-amino-N-ribosylacetamide 5'-phosphate kinosynthase
* 5'-phosphoribosylglycinamide synthetase
* GAR synthetase
Mechanism
GARS operates via an ordered, sequential mechanism. 5-phospho-D-ribosylamine (PRA) binds first, then ATP, and finally glycine. Phosphate is released first, followed by ADP and GAR.
The oxygen in the
ribose
Ribose is a simple sugar and carbohydrate with molecular formula C5H10O5 and the linear-form composition H−(C=O)−(CHOH)4−H. The naturally occurring form, , is a component of the ribonucleotides from which RNA is built, and so this comp ...
ring of PRA is important in substrate binding, likely due to favorable energetics from
hydrogen bond
In chemistry, a hydrogen bond (H-bond) is a specific type of molecular interaction that exhibits partial covalent character and cannot be described as a purely electrostatic force. It occurs when a hydrogen (H) atom, Covalent bond, covalently b ...
ing and the ring conformation it confers.
In addition, the phosphate group of GAR has been implicated in GARS substrate recognition.
The reaction starts with the oxygen of glycine acting as a
nucleophile
In chemistry, a nucleophile is a chemical species that forms bonds by donating an electron pair. All molecules and ions with a free pair of electrons or at least one pi bond can act as nucleophiles. Because nucleophiles donate electrons, they are ...
to attack the γ-phosphorus of ATP. Then, the nitrogen of PRA attacks the carbonyl carbon in the intermediate, and phosphate leaves, forming GAR.
Structural studies
As of late 2007, 3
structures
A structure is an arrangement and organization of interrelated elements in a material object or system, or the object or system so organized. Material structures include man-made objects such as buildings and machines and natural objects such as ...
have been solved for this class of enzymes, with
PDB accession codes , , and . The overall structure of the enzyme, based on crystallization from ''
E. coli
''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escherichia'' that is commonly foun ...
'',
consists of 16
alpha helices
An alpha helix (or α-helix) is a sequence of amino acids in a protein that are twisted into a coil (a helix).
The alpha helix is the most common structural arrangement in the secondary structure of proteins. It is also the most extreme type of l ...
which connect to 20
beta strand
The beta sheet (β-sheet, also β-pleated sheet) is a common structural motif, motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone chain, backbon ...
s by turns and loops. There are four main domains: N, A, B, and C. Each domain has a central
beta sheet
The beta sheet (β-sheet, also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a gene ...
with an alpha helix on at least one side. The N, A, and C domains are clustered together, while the B domain is slightly separated from the others and connected to them by two hinge regions. The active site is between the NAC group and the B domain. The A and B domains appear to facilitate ATP binding, while the N and C domains confer substrate specificity. The N domain is very similar to that of glycinamide ribonucleotide transformylase. Although the orientation of the B domains varies, the structure of GARS is very similar across organisms.
Furthermore, the gene has been sequenced in many organisms, and ''E. coli'' shows between 41 and 52% identity with the GARS sequences of ''
B. subtilis
''Bacillus subtilis'' (), known also as the hay bacillus or grass bacillus, is a gram-positive, catalase-positive bacterium, found in soil and the gastrointestinal tract of ruminants, humans and marine sponges. As a member of the genus ''Bacill ...
'', ''
S. cerevisiae
''Saccharomyces cerevisiae'' () (brewer's yeast or baker's yeast) is a species of yeast (single-celled fungal microorganisms). The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been o ...
'', ''
D. melanogaster'', and ''
D. pseudobscura''.
Human GARS-AIRS-GART has been shown to be most similar to that of mice, chimpanzees, and cows.
Among the amino acids that are identical in ''B. subtilis'', ''S. cerevisiae'', ''D. melanogaster'', and ''D. pseudobscura'', almost a third are glycine and
proline
Proline (symbol Pro or P) is an organic acid classed as a proteinogenic amino acid (used in the biosynthesis of proteins), although it does not contain the amino group but is rather a secondary amine. The secondary amine nitrogen is in the p ...
, which suggests that they play an important role in proper
folding
Fold, folding or foldable may refer to:
Arts, entertainment, and media
* ''Fold'' (album), the debut release by Australian rock band Epicure
* Fold (poker), in the game of poker, to discard one's hand and forfeit interest in the current pot
*Abov ...
of the protein.
In addition to similar structure across species, GARS as a whole has a very similar structure to
D-alanine:D-alanine ligase,
biotin carboxylase
In enzymology, a biotin carboxylase () is an enzyme that catalyzes the chemical reaction
: ATP + biotin-carboxyl-carrier protein + CO2 \rightleftharpoons ADP + phosphate + carboxybiotin-carboxyl-carrier protein
The three substrates of this e ...
, and
glutathione synthetase
Glutathione synthetase (GSS) () is the second enzyme in the glutathione (GSH) biosynthesis pathway. It catalyses the condensation of gamma-glutamylcysteine and glycine, to form glutathione. Glutathione synthetase is also a potent antioxidan ...
. All of these enzymes have an ATP binding domain classified as
ATP-grasp
In molecular biology, the ATP-grasp fold is a unique ATP-binding protein structural motif made of two α+ β subdomains that "grasp" a molecule of ATP between them. ATP-grasp proteins have ATP-dependent carboxylate-amine/thiol ligase activity ...
domains.
Disease relevance
In humans, the gene that codes for GARS-AIRS-GART is on
chromosome 21
Chromosome 21 is one of the 23 pairs of chromosomes in humans. Chromosome 21 is both the smallest human autosome and chromosome, with 46.7 million base pairs (the building material of DNA) representing about 1.5 percent of the total DNA in cell ...
, and individuals with
Down Syndrome have higher purine levels, which has been correlated with mental retardation. Thus, studies have been conducted to investigate its involvement in Down Syndrome. It has been found that GARS is expressed for longer in individuals with Down Syndrome than in unaffected individuals.
In unaffected individuals, GARS is highly expressed in the
cerebellum
The cerebellum (: cerebella or cerebellums; Latin for 'little brain') is a major feature of the hindbrain of all vertebrates. Although usually smaller than the cerebrum, in some animals such as the mormyrid fishes it may be as large as it or eve ...
before birth but is barely expressed by three weeks after birth. In individuals with Down Syndrome, GARS expression continues until at least seven weeks after birth. This suggests that GARS may be a main contributor to the development of Down Syndrome. However, so far no
mutations
In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, mitosi ...
to GARS have been identified that could change its function and cause Down Syndrome related mental retardation.
References
{{DEFAULTSORT:Phosphoribosylamine-glycine ligase
EC 6.3.4
Enzymes of known structure