Phosphoribosylamine-glycine ligase
Encyclopedia
In enzymology, a phosphoribosylamine-glycine ligase is an enzyme
that catalyzes
the chemical reaction
The 3 substrates
of this enzyme are ATP
, 5-phospho-D-ribosylamine, and glycine
, whereas its 3 products
are ADP
, phosphate
, and N1-(5-phospho-D-ribosyl)glycinamide.
This enzyme belongs to the family of ligase
s, specifically those forming generic carbon-nitrogen bonds. This enzyme participates in purine metabolism
.
Bacterial
genes that encode this enzyme are often named purD. The purD genes often contain PurD RNA motif
in their 5' UTR
.
In bacteria, GARS is a monofunctional enzyme
(encoded by the purD gene). In yeast
, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS and with phosphoribosylglycinamide formyltransferase
(GART), forming GARS-AIRS-GART.
have been solved for this class of enzymes, with PDB
accession codes , , and .
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
that catalyzes
Catalysis
Catalysis is the change in rate of a chemical reaction due to the participation of a substance called a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. A catalyst may participate in multiple chemical transformations....
the chemical reaction
Chemical reaction
A chemical reaction is a process that leads to the transformation of one set of chemical substances to another. Chemical reactions can be either spontaneous, requiring no input of energy, or non-spontaneous, typically following the input of some type of energy, such as heat, light or electricity...
- ATP + 5-phospho-D-ribosylamine + glycine
ADP + phosphate + N1-(5-phospho-D-ribosyl)glycinamide
The 3 substrates
Substrate (biochemistry)
In biochemistry, a substrate is a molecule upon which an enzyme acts. Enzymes catalyze chemical reactions involving the substrate. In the case of a single substrate, the substrate binds with the enzyme active site, and an enzyme-substrate complex is formed. The substrate is transformed into one or...
of this enzyme are ATP
Adenosine triphosphate
Adenosine-5'-triphosphate is a multifunctional nucleoside triphosphate used in cells as a coenzyme. It is often called the "molecular unit of currency" of intracellular energy transfer. ATP transports chemical energy within cells for metabolism...
, 5-phospho-D-ribosylamine, and glycine
Glycine
Glycine is an organic compound with the formula NH2CH2COOH. Having a hydrogen substituent as its 'side chain', glycine is the smallest of the 20 amino acids commonly found in proteins. Its codons are GGU, GGC, GGA, GGG cf. the genetic code.Glycine is a colourless, sweet-tasting crystalline solid...
, whereas its 3 products
Product (chemistry)
Product are formed during chemical reactions as reagents are consumed. Products have lower energy than the reagents and are produced during the reaction according to the second law of thermodynamics. The released energy comes from changes in chemical bonds between atoms in reagent molecules and...
are ADP
Adenosine diphosphate
Adenosine diphosphate, abbreviated ADP, is a nucleoside diphosphate. It is an ester of pyrophosphoric acid with the nucleoside adenosine. ADP consists of the pyrophosphate group, the pentose sugar ribose, and the nucleobase adenine....
, phosphate
Phosphate
A phosphate, an inorganic chemical, is a salt of phosphoric acid. In organic chemistry, a phosphate, or organophosphate, is an ester of phosphoric acid. Organic phosphates are important in biochemistry and biogeochemistry or ecology. Inorganic phosphates are mined to obtain phosphorus for use in...
, and N1-(5-phospho-D-ribosyl)glycinamide.
This enzyme belongs to the family of ligase
Ligase
In biochemistry, ligase is an enzyme that can catalyse the joining of two large molecules by forming a new chemical bond, usually with accompanying hydrolysis of a small chemical group dependent to one of the larger molecules...
s, specifically those forming generic carbon-nitrogen bonds. This enzyme participates in purine metabolism
Purine metabolism
-Biosynthesis:Purines are biologically synthesized as nucleotides and in particular as ribotides, i.e. bases attached to ribose 5-phosphate. A key regulatory step is the production of 5-phospho-α-D-ribosyl 1-pyrophosphate by PRPP synthetase, which is activated by inorganic phosphate and...
.
Bacterial
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
genes that encode this enzyme are often named purD. The purD genes often contain PurD RNA motif
PurD RNA motif
The purD RNA motif is a conserved RNA structure found in epsilonproteobacteria, such as the genera Helicobacter and Campylobacter. The RNA is consistently found in the apparent 5' UTR of purD genes. purD genes encode the enzyme Phosphoribosylamine-glycine ligase, which catalyzes an early step in...
in their 5' UTR
Five prime untranslated region
A messenger ribonucleic acid molecule codes for a protein through translation. The mRNA also contains regions that are not translated: in eukaryotes these include the 5' untranslated region, 3' untranslated region, 5' cap and poly-A tail....
.
In bacteria, GARS is a monofunctional enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
(encoded by the purD gene). In yeast
Yeast
Yeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with 1,500 species currently described estimated to be only 1% of all fungal species. Most reproduce asexually by mitosis, and many do so by an asymmetric division process called budding...
, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS and with phosphoribosylglycinamide formyltransferase
Phosphoribosylglycinamide formyltransferase
Trifunctional purine biosynthetic protein adenosine-3 is an enzyme that in humans is encoded by the GART gene.This protein is a trifunctional polypeptide...
(GART), forming GARS-AIRS-GART.
Nomenclature
The systematic name 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, and
- GAR.
Structural studies
As of late 2007, 3 structuresTertiary structure
In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.-Relationship to primary structure:...
have been solved for this class of enzymes, with PDB
Protein Data Bank
The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids....
accession codes , , and .