Amidophosphoribosyltransferase

Phosphoribosyl pyrophosphate amidotransferase
Structure of the ATase tetramer, generated from 1ECB.
Identifiers
Symbols	PPAT ; ATASE; GPAT; PRAT
External IDs	OMIM: 172450 MGI: 2387203 HomoloGene: 68272 IUPHAR: 2761 GeneCards: PPAT Gene
EC number	2.4.2.14
Gene ontology Molecular function • amidophosphoribosyltransferase activity • metal ion binding • 4 iron, 4 sulfur cluster binding Cellular component • cytosol Biological process • G1/S transition of mitotic cell cycle • kidney development • purine nucleobase metabolic process • purine nucleotide biosynthetic process • 'de novo' IMP biosynthetic process • glutamine catabolic process • lactation • purine nucleobase biosynthetic process • nucleoside metabolic process • purine ribonucleoside monophosphate biosynthetic process • organ regeneration • cellular response to insulin stimulus • cellular response to drug • small molecule metabolic process • protein homotetramerization • nucleobase-containing small molecule metabolic process • maternal process involved in female pregnancy Sources: Amigo / QuickGO
Orthologs
Species	Human	Mouse
Entrez	5471	231327
Ensembl	ENSG00000128059	ENSMUSG00000029246
UniProt	Q06203	Q3UGU3
RefSeq (mRNA)	NM_002703	NM_172146
RefSeq (protein)	NP_002694	NP_742158
Location (UCSC)	Chr 4: 56.39 – 56.44 Mb	Chr 5: 76.91 – 76.95 Mb
PubMed search	[1]	[2]

Amidophosphoribosyltransferase (ATase), also known as glutamine phosphoribosylpyrophosphate amidotransferase (GPAT), is an enzyme responsible for catalyzing the conversion of 5-phosphoribosyl-1-pyrophosphate (PRPP) into 5-phosphoribosyl-1-amine (PRA), using the ammonia group from a glutamine side-chain. This is the committing step in de novo purine synthesis. In humans it is encoded by the PPAT (phosphoribosyl pyrophosphate amidotransferase) gene. ATase is a member of the purine/pyrimidine phosphoribosyltransferase family.

Structure and function

amidophosphoribosyltransferase
Identifiers
EC number	2.4.2.14
CAS number	Template:CAS
Databases
IntEnz	IntEnz view
BRENDA	BRENDA entry
ExPASy	NiceZyme view
KEGG	KEGG entry
MetaCyc	metabolic pathway
PRIAM	profile
PDB structures	RCSB PDB PDBe PDBsum
Gene Ontology	AmiGO / EGO
Search PMC articles PubMed articles NCBI proteins

The enzyme consists of two domains: a glutaminase domain that produces ammonia from glutamine by hydrolysis and a phosphoribosyltransferase domain that binds the ammonia to ribose-5-phosphate. Coordination between the two active sites of enzyme give it special complexity.

The glutaminase domain is homologous to other N-terminal nucleophile (Ntn) hydrolases such as carbamoyl phosphate synthetase (CPSase). Nine invariant residues among the sequences of all Ntn amidotransferases play key catalytic, substrate binding or structural roles. A terminal cysteine residue acts as the nucleophile in the first part of the reaction, analogous to the cysteine of a catalytic triad. The free N terminus acts as a base to activate the nucleophile and protonate the leaving group in the hydrolytic reaction, in this case ammonia. Another key aspect of the catalytic site is an oxyanion hole which catalyzes the reaction intermediate, as shown in the mechanism below.

The PRTase domain is homologous to many other PRTases involved in the purine nucleotide synthesis and salvage pathways. All PRTases involve the displacement of pyrophosphate in PRPP by a variety of nucleophiles. ATase is the only PRTase that has ammonia as a nucleophile. Pyrophosphate from PRPP is an excellent leaving group, so little chemical assistance is needed to promote catalysis. Rather, the primary function of the enzyme appears to be bringing the reactants together appropriately and preventing the wrong reaction, such as hydrolysis.

Besides having their respective catalytic abilities, the two domains also coordinate with one another to ensure that all the ammonia produced from glutamine is transferred to PRPP and no other nucleophile than ammonia attacks PRPP. This is achieved mainly by blocking formation of ammonia until PRPP is bound and channelling the ammonia to the PRTase active site.

Initial activation of the enzyme by PRPP is caused by a conformational change in a "glutamine loop", which repositions to be able to accept glutamine. This results in a 200-fold higher K_m value for glutamine binding Once glutamine has bound to the active site, further conformational changes bring the site into the enzyme, making it inaccessible.

These conformational changes also result in the formation of a 20 Å long ammonia channel, one of the most striking features of this enzyme. This channel lacks any hydrogen bonding sites, to ensure easy diffusion of ammonia from one active site to the other. This channel ensures ammonia released from glutamine reaches the PRTase catalytic site, and it differs from the channel in CPSase in that it is hydrophobic rather than polar, and transient rather than permanent.

Reaction mechanism

First half of the catalytic mechanism of ATase occurring in the glutaminase domain active site. The catalytic cysteine perfoms a nucleophilic attack on the substrate to form an acyl-enzyme intermediate, which is resolved by hydrolysis. Ammonia is produced in the third step, which is used in the second half of the mechanism.

Second half of the catalytic mechanism of ATase occurring in the phosphoribosyltransferase domain active site. The ammonia liberated in the first half of the reaction replaces pyrophosphate in PRPP, yielding phosphoribosylamine. A tyrosine residue stabilizes the transition state and allows the reaction to occur.

The overall reaction catalyzed by ATase is the following:

PRPP + glutamine → PRA + glutamate + PPi

Within the enzyme, the reaction is broken down into two half reactions that occur at different active sites:

1. glutamine → NH
   ₃ + glutamate
2. PRPP + NH
   ₃ → PRA + PPi

The first part of the mechanism occurs in the active site of the glutaminase domain and releases an ammonia group from glutamine by hydrolysis. The ammonia released by the first reaction is then transferred to the active site of the phosphoribosyltransferase domain via a 20 Å channel, where it then binds to PRPP to form PRA.

Regulation

In an example of feedback inhibition, ATase is inhibited mainly by the end-products of the purine synthesis pathway, AMP, GMP, ADP, and GDP. Each enzyme subunit from the homotetramer has two binding sites for these inhibitors. The allosteric (A) site overlaps with the site for the ribose-5-phosphate of PRPP, while the catalytic (C) site overlaps with the site for the pyrophosphate of PRPP. The binding of specific nucleotide pairs to the two sites results in synergistic inhibition stronger than additive inhibition. Inhibition occurs via a structural change in the enzyme where the flexible glutamine loop gets locked in an open position, preventing the binding of PRPP.

Due to the chemical lability of PRA, which has a half-life of 38 seconds at PH 7.5 and 37 °C, researchers have suggested that the compound is channeled from Amidophosphoribosyltransferase to GAR synthetase in vivo.

Interactive pathway map

Click on genes, proteins and metabolites below to link to respective articles.

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|{{{bSize}}}px|alt=Fluorouracil (5-FU) Activity edit]]

File:FluoropyrimidineActivity_WP1601.png

Fluorouracil (5-FU) Activity edit

Gallery

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  PRPP

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  5-phosphoribosylamine

External links

• Amidophosphoribosyl transferase at the US National Library of Medicine Medical Subject Headings (MeSH)

This article incorporates text from the United States National Library of Medicine, which is in the public domain.