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Information on EC 2.7.6.1 - ribose-phosphate diphosphokinase and Organism(s) Escherichia coli and UniProt Accession P0A717
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2.7.6.1 ribose-phosphate diphosphokinaseIUBMB Comments
dATP can also act as donor.
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Word Map
- 2.7.6.1
- purine
- erythrocyte
-
superactivity
- pyrimidine
-
x-linked
- phosphoribosyltransferase
-
uric
- gout
- hypoxanthine
-
hypoxanthine-guanine
- deafness
- charcot-marie-tooth
-
sensorineural
-
hemolysates
-
diphosphorylated
-
nonsyndromic
- hgprt
-
hyperuricaemia
- lesch-nyhan
-
phosphoribosyl-pyrophosphate
-
feedback-resistant
- synthesis
- medicine
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
prps1, prpp synthetase, phosphoribosylpyrophosphate synthetase, phosphoribosyl pyrophosphate synthetase, prpp synthase, prpps, prs-i, ribose-phosphate pyrophosphokinase, ppribp synthetase, 5-phosphoribosyl-1-pyrophosphate synthetase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
5-phosphoribose pyrophosphorylase
-
-
-
-
5-phosphoribosyl-1-pyrophosphate synthetase
-
-
-
-
5-phosphoribosyl-alpha-1-pyrophosphate synthetase
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-
-
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ATP:D-ribose-5-phosphate pyrophosphotransferase
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-
-
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phosphoribosyl-diphosphate synthetase
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-
-
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phosphoribosylpyrophosphate synthase
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-
-
-
phosphoribosylpyrophosphate synthetase
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-
-
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PP-ribose P synthetase
-
-
-
-
PPRibP synthetase
-
-
-
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PRPP synthase
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-
-
-
PRPP synthetase
-
-
-
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pyrophosphokinase, ribose phosphate
-
-
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pyrophosphoribosylphosphate synthetase
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-
-
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ribophosphate pyrophosphokinase
-
-
-
-
ribose-5-phosphate pyrophosphokinase
-
-
-
-
ribose-phosphate pyrophosphokinase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + D-ribose 5-phosphate = AMP + 5-phospho-alpha-D-ribose 1-diphosphate
mechanism
-
ATP + D-ribose 5-phosphate = AMP + 5-phospho-alpha-D-ribose 1-diphosphate
steady state ordered mechanism in which Mg2+ binds first and D-ribose 5-phosphate binds last
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
diphosphate transfer
-
-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
KEGG
-
-
SYSTEMATIC NAME
IUBMB Comments
ATP:D-ribose-5-phosphate diphosphotransferase
dATP can also act as donor.
CAS REGISTRY NUMBER
COMMENTARY
9015-83-2
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + D-ribose 5-phosphate
AMP + 5-phospho-alpha-D-ribose 1-diphosphate
-
-
-
?
(R)9-(2-phosphonylmethoxypropyl)adenine + 5-phospho-alpha-D-ribose 1-diphosphate
(R)9-(2-phosphonylmethoxypropyl)adenine-diphosphate + D-ribose 5-phosphate
-
-
-
r
(R)9-(3-fluoro-2-phosphonylmethoxypropyl)adenine + 5-phospho-alpha-D-ribose 1-diphosphate
(R)9-(3-fluoro-2-phosphonylmethoxypropyl)adenine-diphosphate + D-ribose 5-phosphate
-
-
-
r
(S)9-(2-phosphonylmethoxypropyl)adenine + 5-phospho-alpha-D-ribose 1-diphosphate
(S)9-(2-phosphonylmethoxypropyl)adenine-diphosphate + D-ribose 5-phosphate
-
-
-
r
(S)9-(3-fluoro-2-phosphonylmethoxypropyl)adenine + 5-phospho-alpha-D-ribose 1-diphosphate
(S)9-(3-fluoro-2-phosphonylmethoxypropyl)adenine-diphosphate + D-ribose 5-phosphate
-
-
-
r
2',3'-dideoxy-2',3'-didehydro-adenosine-5'-monophosphate + 5-phospho-alpha-D-ribose 1-diphosphate
2',3'-dideoxy-2',3'-didehydro-adenosine-5'-triphosphate + D-ribose 5-phosphate
-
-
-
r
9-(2-phosphonylmethoxyethoxy)adenine + 5-phospho-alpha-D-ribose 1-diphosphate
9-(2-phosphonylmethoxyethoxy)adenine-diphosphate + D-ribose 5-phosphate
-
-
-
r
9-(2-phosphonylmethoxyethyl)adenine + 5-phospho-alpha-D-ribose 1-diphosphate
9-(2-phosphonylmethoxyethyl)adenine-diphosphate + D-ribose 5-phosphate
-
-
-
r
AMP + 5-phospho-alpha-D-ribose 1-diphosphate
ATP + D-ribose 5-phosphate
-
-
-
r
ATP + D-ribose 5-phosphate
AMP + 5-phospho-alpha-D-ribose 1-diphosphate
-
-
-
r
ATP + D-ribose 5-phosphate
AMP + 5-phospho-alpha-D-ribose 1-diphosphate
-
-
-
r
ATP + D-ribose 5-phosphate
AMP + 5-phospho-alpha-D-ribose 1-diphosphate
-
-
-
r
ATP + D-ribose 5-phosphate
AMP + 5-phospho-alpha-D-ribose 1-diphosphate
-
-
ribose product also known as 5-phosphoryl-D-ribofuranose alpha-1-diphosphate
r
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + D-ribose 5-phosphate
AMP + 5-phospho-alpha-D-ribose 1-diphosphate
-
-
-
?
ATP + D-ribose 5-phosphate
AMP + 5-phospho-alpha-D-ribose 1-diphosphate
-
-
-
r
ATP + D-ribose 5-phosphate
AMP + 5-phospho-alpha-D-ribose 1-diphosphate
-
-
-
r
ATP + D-ribose 5-phosphate
AMP + 5-phospho-alpha-D-ribose 1-diphosphate
-
-
-
r
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mg2+
-
saturation with free Mg2+ results in hyperbolic activation by phosphate. At unsaturating free Mg2+ concentration, cooperative activation by phosphate is observed
Mg2+
-
prepares the active site of the enzyme for the binding of the highly phosphorylated ligands
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.377
2',3'-dideoxy-2',3'-didehydro-adenosine-5'-monophosphate
-
pH 8.0, 37ºC
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.55
2',3'-dideoxy-2',3'-didehydro-adenosine-5'-monophosphate
-
pH 8.0, 37ºC
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
the enzyme belongs to the phosphoribosyl diphosphate synthetase family, enzymes of this family are widespread in different eukaryotic and prokaryotic organisms and are involved in a number of important biochemical processes associated with purine and pyrimidine metabolism
physiological function
the enzyme produces 5-phosphoribosyl diphosphate which is an essential metabolite and an allosteric regulator in the de novo and salvage pathways of the biosynthesis of purine and pyrimidine nucleotides, pyrimidine-containing enzyme cofactors, and the amino acids histidine and tryptophan. Due to the key role of the enzyme in cell metabolism, the activity of these enzymes is tightly regulated by an excess of the substrate via feedback inhibition, as well as by allosteric interactions through the binding of ADP or GDP molecules in a special site between the subunits of the enzyme
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
x * 34288, sequence calculation, three-dimensional structure analysis
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified enzyme, hanging drop vapor diffusion technique by mixing of 0.001 ml of 10 mg/mL protein in 0.02 M Tris-HCl buffer, pH 7.5, containing 0.04% NaN3, with 0.001 ml of reservoir solution containing from 18% (NH4)2SO4, 0.02 M Tris-HCl buffer, pH 7.5, 0.02 mM MgCl2 and 0.02 mM ATP, screening and optimization to capillary counter-diffusion technique, largest crystals are obtained using a protein solution with a protein concentration of 14 mg/mL in 0.02 M Tris-HCl buffer, pH 7.5, containing 2 mM MgCl2, 2 mM ATP, and 0.04% NaN3, and a reservoir solution composed of 14% ammonium sulfate in 0.1 M Tris buffer, pH 8.5, containing 0.3 M NaCl, 2 mM MgCl2, and 0.04% NaN3, X-ray diffraction structure determination and analysis at 3.1 A resolution
structure to 2.71 A resolution, of single crystals grown under microgravity. The monomers are assembled into a hexamer with 32 point symmetry. The N-terminal regions of the subunits are located near the threefold axis and form a propeller-like structure in which each subunit interacts with two adjacent subunits in different manner
to 2.2 A resolution. The protein has two type I phosphoribosyltransferase folds, related by 2fold pseudosymmetry. The propeller-shaped homohexameric structure is composed of a trimer of dimers, with the C-terminal domains forming the dimeric blades of the propeller and the N-terminal domains forming the hexameric core. Several residues from a flexible loop occupy the site where the allosteric modulator, adenosine diphosphate, is predicted to bind
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
G9S
-
mutation originates from prs-2 allele variant which is related to thermosensitive growth, decreased activity in comparison to the wild-type
K194A
-
mutation in conserved lysine residue, results in protein variant unable to synthetize 5-phospho-alpha-D-ribose 1-diphosphate
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
stored and diluted in the presence of phosphate 50 mM to maintain stability. With 2 mM MgATP2- or more, the enzyme is fully stable upon dilution and subsequent incubation at 37ºC
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
synthesis
-
expression of Escherichia coli Prs protein in Rosetta (DE3) and BL21 (DE3) pLysE strains and detailed method for His-Prs and untagged Prs purification on nickel affinity chromatography columns. The protocol allows purification of proteins with high yield, purity and activity
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Switzer, R.L.
Phosphoribosylpyrophosphate synthetase and related pyrophosphokinases
The Enzymes,3rd Ed. (Boyer,P. D. ,ed. )
10
607-629
1974
Gallus gallus, Columba sp., Escherichia coli, Homo sapiens, Mus musculus, Ophiodon elongatus, Rattus norvegicus, Salmonella enterica subsp. enterica serovar Typhimurium
-
Balzarini, J.; Nave, J.F.; Becker, M.A.; Tatibana, M.; De Clercq, E.
Kinetic properties of adenine nucleotide analogs against purified 5-phosphoribosyl-1-pyrophosphate synthetase from E. coli, rat liver and human erythrocytes
Nucleosides Nucleotides
14
1861-1871
1995
Escherichia coli, Homo sapiens, Rattus norvegicus
-
Willemoes, M.; Hove-Jensen, B.
Binding of divalent magnesium by Escherichia coli phosphoribosyl diphosphate synthetase
Biochemistry
36
5078-5083
1997
Escherichia coli
Willemoes, M.; Hove-Jensen, B.; Larsen, S.
Steady state kinetic model for the binding of substrates and allosteric effectors to Escherichia coli phosphoribosyl-diphosphate synthase
J. Biol. Chem.
275
35408-35412
2000
Escherichia coli
Timofeev, V.; Abramchik, Y.; Zhukhlistova, N.; Kuranova, I.
Crystallization and preliminary X-ray diffraction study of phosphoribosyl pyrophosphate synthetase from E. coli
Crystallogr. Rep.
60
685-688
2015
Escherichia coli (P0A717)
-
Zhou, W.; Tsai, A.; Dattmore, D.; Stives, D.; Chitrakar, I.; DAlessandro, A.; Patil, S.; Hicks, K.; French, J.
Crystal structure of E. coli PRPP synthetase
BMC Struct. Biol.
19
001
2019
Escherichia coli (P0A719), Escherichia coli
Timofeev, V.; Abramchik, Y.; Zhukhlistova, N.; Muravieva, T.; Esipov, R.; Kuranova, I.
Three-dimensional structure of phosphoribosyl pyrophosphate synthetase from E. coli at 2.71 A resolution
Crystallogr. Rep.
61
44-54
2016
Escherichia coli (P0A717)
-
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