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47  structures 7914  species 3  interactions 11512  sequences 64  architectures

Family: Pribosyl_synth (PF14572)

Summary: Phosphoribosyl synthetase-associated domain

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This is the Wikipedia entry entitled "Ribose-phosphate diphosphokinase". More...

Ribose-phosphate diphosphokinase Edit Wikipedia article

Ribose-phosphate diphosphokinase
Phosphoribosyl pyrophosphate synthase 1, hexamer, Human
EC number
CAS number 9031-46-3
IntEnz IntEnz view
ExPASy NiceZyme view
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / QuickGO
phosphoribosyl pyrophosphate synthetase 1
Symbol PRPS1
Entrez 5631
HUGO 9462
OMIM 311850
RefSeq NM_002764
UniProt P60891
Other data
EC number
Locus Chr. X q21-q27
phosphoribosyl pyrophosphate synthetase 2
Symbol PRPS2
Entrez 5634
HUGO 9465
OMIM 311860
RefSeq NM_002765
UniProt P11908
Other data
EC number
Locus Chr. X pter-q21

Ribose-phosphate diphosphokinase (or phosphoribosyl pyrophosphate synthetase or ribose-phosphate pyrophosphokinase) is an enzyme that converts ribose 5-phosphate into phosphoribosyl pyrophosphate (PRPP).[1][2] It is classified under EC

The enzyme is involved in the synthesis of nucleotides (purines and pyrimidines), cofactors NAD and NADP, and amino acids histidine and tryptophan,[1][2][3] linking these biosynthetic processes to the pentose phosphate pathway, from which the substrate ribose 5-phosphate is derived. Ribose 5-phosphate is produced by the HMP Shunt Pathway from Glucose-6-Phosphate. The product phosphoribosyl pyrophosphate acts as an essential component of the purine salvage pathway and the de novo synthesis of purines. Dysfunction of the enzyme would thereby undermine purine metabolism. Ribose-phosphate pyrophosphokinase exists in bacteria, plants, and animals, and there are three isoforms of human ribose-phosphate pyrophosphokinase.[2] In humans, the genes encoding the enzyme are located on the X chromosome.[2]

Reaction mechanism

Overall reaction for phosphoribosyl pyrophosphate synthetase

Ribose-phosphate diphosphokinase transfers the diphosphoryl group from Mg-ATP (Mg2+ coordinated to ATP) to ribose 5-phosphate.[2] The enzymatic reaction begins with the binding of ribose 5-phosphate, followed by binding of Mg-ATP to the enzyme. In the transition state upon binding of both substrates, the diphosphate is transferred. The enzyme first releases AMP before releasing the product phosphoribosyl pyrophosphate.[4] Experiments using oxygen 18 labelled water demonstrate that the reaction mechanism proceeds with the nucleophilic attack of the anomeric hydroxyl group of ribose 5-phosphate on the beta-phosphorus of ATP in an SN2 reaction.[5]

SN2 mechanism of phosphoribosyl pyrophosphate synthetase


PyMol rendering of one subunit of the enzyme phosphoribosyl pyrophosphate synthetase I (human). Flexible loop colored in green; ribose 5-phosphate binding region colored in blue.
PyMol rendering of phosphoribosyl pyrophosphate synthetase I (human) as a homodimer, formed by two subunits (red and blue). Three homodimers form the active enzyme complex.

Crystallization and X-ray diffraction studies elucidated the structure of the enzyme, which was isolated by cloning, protein expression, and purification techniques. One subunit of ribose-phosphate diphosphokinase consists of 318 amino acids; the active enzyme complex consists of three homodimers (or six subunits, a hexamer). The structure of one subunit is a five-stranded parallel beta sheet (the central core) surrounded by four alpha helices at the N-terminal domain and five alpha helices at the C-terminal domain, with two short anti-parallel beta-sheets extending from the core.[2] The catalytic site of the enzyme binds ATP and ribose 5-phosphate. The flexible loop (Phe92–Ser108), pyrophosphate binding loop (Asp171–Gly174), and flag region (Val30–Ile44 from an adjacent subunit) comprise the ATP binding site, located at the interface between two domains of one subunit. The flexible loop is so named because of the its large variability in conformation.[6] The ribose 5-phosphate binding site consists of residues Asp220–Thr228, located in the C-terminal domain of one subunit.[2][6] The allosteric site, which binds ADP, consists of amino acid residues from three subunits.[2]


The product of this reaction, phosphoribosyl pyrophosphate (PRPP), is used in numerous biosynthesis (de novo and salvage) pathways. PRPP provides the ribose sugar in de novo synthesis of purines and pyrimidines, used in the nucleotide bases that form RNA and DNA. PRPP reacts with orotate to form orotidylate, which can be converted to uridylate (UMP). UMP can then be converted to the nucleotide cytidine triphosphate (CTP). The reaction of PRPP, glutamine, and ammonia forms 5-Phosphoribosyl-1-amine, a precursor to inosinate (IMP), which can ultimately be converted to adenosine triphosphate (ATP) or guanosine triphosphate (GTP). PRPP plays a role in purine salvage pathways by reacting with free purine bases to form adenylate, guanylate, and inosinate.[7][8] PRPP is also used in the synthesis of NAD: the reaction of PRPP with nicotinic acid yields the intermediate nicotinic acid mononucleotide.[9]


Ribose-phosphate diphosphokinase requires Mg2+ for activity; the enzyme acts only on ATP coordinated with Mg2+. Ribose-phosphate diphosphokinase is regulated by phosphorylation and allostery. It is activated by phosphate and inhibited by ADP; it is suggested that phosphate and ADP compete for the same regulatory site. At normal concentrations, phosphate activates the enzyme by binding to its allosteric regulatory site. However, at high concentrations, phosphate is shown to have an inhibitory effect by competing with the substrate ribose 5-phosphate for binding at the active site. ADP is the key allosteric inhibitor of ribose-phosphate diphosphokinase. It has been shown that at lower concentrations of the substrate ribose 5-phosphate, ADP may inhibit the enzyme competitively. Ribose-phosphate pyrophosphokinase is also inhibited by some of its downstream biosynthetic products.[2][6]

Role in disease

Because its product is a key compound in many biosynthetic pathways, ribose-phosphate diphosphokinase is involved in some rare disorders and X-linked recessive diseases. Mutations that lead to super-activity (increased enzyme activity or de-regulation of the enzyme) result in purine and uric acid overproduction. Super-activity symptoms include gout, sensorineural hearing loss,[10] weak muscle tone (hypotonia), impaired muscle coordination (ataxia), hereditary peripheral neuropathy,[11] and neurodevelopmental disorder.[12][13][14] Mutations that lead to loss-of-function in ribose-phosphate diphosphokinase result in Charcot-Marie-Tooth disease and ARTS syndrome.[15]


  1. ^ a b Visentin LP, Hasnain S, Gallin W (July 1977). "Ribosomal protein S1/S1A in bacteria". FEBS Lett. 79 (2): 258–63. doi:10.1016/0014-5793(77)80799-0. PMID 330231. 
  2. ^ a b c d e f g h i Li S, Lu Y, Peng B, Ding J (January 2007). "Crystal structure of human phosphoribosylpyrophosphate synthetase 1 reveals a novel allosteric site". Biochem. J. 401 (1): 39–47. doi:10.1042/BJ20061066. PMC 1698673Freely accessible. PMID 16939420. 
  3. ^ Tang W, Li X, Zhu Z, Tong S, Li X, Zhang X, Teng M, Niu L (May 2006). "Expression, purification, crystallization and preliminary X-ray diffraction analysis of human phosphoribosyl pyrophosphate synthetase 1 (PRS1)". Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 62 (Pt 5): 432–4. doi:10.1107/S1744309106009067. PMC 2219982Freely accessible. PMID 16682768. 
  4. ^ Fox IH, Kelley WN (April 1972). "Human phosphoribosylpyrophosphate synthetase. Kinetic mechanism and end product inhibition". J. Biol. Chem. 247 (7): 2126–31. PMID 4335863. 
  5. ^ Miller GA, Rosenzweig S, Switzer RL (December 1975). "Oxygen-18 studies of the mechanism of pyrophosphoryl group transfer catalyzed by phosphoribosylpyrophosphate synthetase". Arch. Biochem. Biophys. 171 (2): 732–6. doi:10.1016/0003-9861(75)90086-7. PMID 173242. 
  6. ^ a b c Eriksen TA, Kadziola A, Bentsen AK, Harlow KW, Larsen S (April 2000). "Structural basis for the function of Bacillus subtilis phosphoribosyl-pyrophosphate synthetase". Nat. Struct. Biol. 7 (4): 303–8. doi:10.1038/74069. PMID 10742175. 
  7. ^ Fox IH, Kelley WN (March 1971). "Phosphoribosylpyrophosphate in man: biochemical and clinical significance". Ann. Intern. Med. 74 (3): 424–33. doi:10.7326/0003-4819-74-3-424. PMID 4324023. 
  8. ^ Jeremy M. Berg; John L. Tymoczko; Lubert Stryer; Gregory J. Gatto Jr. (2012). Biochemistry (7th ed.). New York: W.H. Freeman. ISBN 1429229365. 
  9. ^ Rongvaux A, Andris F, Van Gool F, Leo O (July 2003). "Reconstructing eukaryotic NAD metabolism". BioEssays. 25 (7): 683–90. doi:10.1002/bies.10297. PMID 12815723. 
  10. ^ Liu X, Han D, Li J, Han B, Ouyang X, Cheng J, Li X, Jin Z, Wang Y, Bitner-Glindzicz M, Kong X, Xu H, Kantardzhieva A, Eavey RD, Seidman CE, Seidman JG, Du LL, Chen ZY, Dai P, Teng M, Yan D, Yuan H (January 2010). "Loss-of-function mutations in the PRPS1 gene cause a type of nonsyndromic X-linked sensorineural deafness, DFN2". Am. J. Hum. Genet. 86 (1): 65–71. doi:10.1016/j.ajhg.2009.11.015. PMC 2801751Freely accessible. PMID 20021999. 
  11. ^ Kim HJ, Sohn KM, Shy ME, Krajewski KM, Hwang M, Park JH, Jang SY, Won HH, Choi BO, Hong SH, Kim BJ, Suh YL, Ki CS, Lee SY, Kim SH, Kim JW (September 2007). "Mutations in PRPS1, which encodes the phosphoribosyl pyrophosphate synthetase enzyme critical for nucleotide biosynthesis, cause hereditary peripheral neuropathy with hearing loss and optic neuropathy (cmtx5)". Am. J. Hum. Genet. 81 (3): 552–8. doi:10.1086/519529. PMC 1950833Freely accessible. PMID 17701900. 
  12. ^ Becker MA, Smith PR, Taylor W, Mustafi R, Switzer RL (November 1995). "The genetic and functional basis of purine nucleotide feedback-resistant phosphoribosylpyrophosphate synthetase superactivity". J. Clin. Invest. 96 (5): 2133–41. doi:10.1172/JCI118267. PMC 185862Freely accessible. PMID 7593598. 
  13. ^ Zoref E, De Vries A, Sperling O (November 1975). "Mutant feedback-resistant phosphoribosylpyrophosphate synthetase associated with purine overproduction and gout. Phosphoribosylpyrophosphate and purine metabolism in cultured fibroblasts". J. Clin. Invest. 56 (5): 1093–9. doi:10.1172/JCI108183. PMC 301970Freely accessible. PMID 171280. 
  14. ^ "Phosphoribosylpyrophosphate synthetase superactivity". Lister Hill National Center for Biomedical Communications. Retrieved 25 February 2014. 
  15. ^ Synofzik M, Müller Vom Hagen J, Haack TB, Wilhelm C, Lindig T, Beck-Wödl S, Nabuurs SB, van Kuilenburg AB, de Brouwer AP, Schöls L (2014). "X-linked Charcot-Marie-Tooth disease, Arts syndrome, and prelingual non-syndromic deafness form a disease continuum: evidence from a family with a novel PRPS1 mutation". Orphanet J Rare Dis. 9 (1): 24. doi:10.1186/1750-1172-9-24. PMC 3931488Freely accessible. PMID 24528855. 

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Phosphoribosyl synthetase-associated domain Provide feedback

This family includes several examples of enzymes from class EC:, phosphoribosyl-pyrophosphate transferase.

Literature references

  1. Katashima R, Iwahana H, Fujimura M, Yamaoka T, Ishizuka T, Tatibana M, Itakura M;, Biochim Biophys Acta. 1998;1396:245-250.: Molecular cloning of a human cDNA for the 41-kDa phosphoribosylpyrophosphate synthetase-associated protein. PUBMED:9545573 EPMC:9545573

  2. Iizasa T;, Nihon Rinsho. 2008;66:694-698.: [Increased activity of PRPP synthetase]. PUBMED:18409517 EPMC:18409517

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005946

Ribose-phosphate diphosphokinase, also known as ribose-phosphate pyrophosphokinase (RPPK), or phosphoribosyldiphosphate synthetase (EC), catalyses the transfer of an intact diphosphate (PP) group from ATP to ribose-5-phosphate (R-5-P), which results in the formation of AMP and 5-phospho-D-ribosyl--1-diphosphate (PRPP).

PRPP is an essential precursor for purine and pyrimidine nucleotides, both in the de novo synthesis and in the salvage pathway, as well as in the synthesis of pyridine nucleotide coenzymes. The activity of PPPK is highly regulated. Besides competitive inhibition at the substrate binding sites, most RPPKs are regulated in an allosteric manner, in which ADP generally acts as the most potent inhibitor. In some systems, close homologues lacking enzymatic activity exist and perform regulatory functions.

Gene Ontology

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Domain organisation

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Pfam Clan

This family is a member of clan PRTase-like (CL0533), which has the following description:

This superfamily of phosphoribosyl-transferases (PRTases) and phosphoribosyl-pyrophosphate synthetase-like protein families is characterised by a core fold of three layers, a/b/a with a mixed beta-sheet of six strands. In one of the families consists of two domains of this fold.

The clan contains the following 7 members:

Pribosyl_synth Pribosyltran Pribosyltran_N PRTase_1 PRTase_2 PRTase_3 UPRTase


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Curation and family details

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Curation View help on the curation process

Seed source: pdb_2c4k; Jackhmmer:Q14558
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 8
Number in full: 11512
Average length of the domain: 128.30 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 38.05 %

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HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 184
Family (HMM) version: 6
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Species distribution

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Archea Archea Eukaryota Eukaryota
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Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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There are 3 interactions for this family. More...

Pribosyltran_N Pribosyl_synth Pribosyltran_N


For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Pribosyl_synth domain has been found. There are 47 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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