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Information on EC 6.3.4.18 - 5-(carboxyamino)imidazole ribonucleotide synthase
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EC Tree
6.3.4.18 5-(carboxyamino)imidazole ribonucleotide synthaseIUBMB Comments
In Escherichia coli, this enzyme, along with EC 5.4.99.18, 5-(carboxyamino)imidazole ribonucleotide mutase, is required to carry out the single reaction catalysed by EC 4.1.1.21, phosphoribosylaminoimidazole carboxylase, in vertebrates. Belongs to the ATP grasp protein superfamily . Carboxyphosphate is the putative acyl phosphate intermediate. Involved in the late stages of purine biosynthesis.
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The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Reaction Schemes
Synonyms
n5-cair synthetase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
N5-CAIR synthetase
N5-carboxyaminoimidazole ribonucleotide synthetase
PurK
additional information
-
PurK is a member of the ATP-grasp protein superfamily
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- + H+ = ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
carboxylation
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PATHWAY SOURCE
PATHWAYS
BRENDA
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SYSTEMATIC NAME
IUBMB Comments
5-amino-1-(5-phospho-D-ribosyl)imidazole:carbon-dioxide ligase (ADP-forming)
In Escherichia coli, this enzyme, along with EC 5.4.99.18, 5-(carboxyamino)imidazole ribonucleotide mutase, is required to carry out the single reaction catalysed by EC 4.1.1.21, phosphoribosylaminoimidazole carboxylase, in vertebrates. Belongs to the ATP grasp protein superfamily [3]. Carboxyphosphate is the putative acyl phosphate intermediate. Involved in the late stages of purine biosynthesis.
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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 + 5-amino-1(5-phospho-D-ribosyl)imidazole + HCO3-
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3-
ADP + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole + phosphate
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3-
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
-
-
-
-
?
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- + H+
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
ATP + 5-amino-1(5-phospho-D-ribosyl)imidazole + HCO3-
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
-
-
-
-
?
ATP + 5-amino-1(5-phospho-D-ribosyl)imidazole + HCO3-
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
-
catalytic steps are the formation of an acyl phosphate intermediate upon ATP cleavage, followed by the nucleophilic attack on the carboxyl carbon of the intermediates by the amino nitrogen of the mononucleotides, formation of acyl phosphate intermediates
-
-
?
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3-
ADP + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole + phosphate
-
assay at pH 7.5, 37°C
-
-
?
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3-
ADP + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole + phosphate
-
assay at pH 7.5, 37°C
-
-
?
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- + H+
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
-
-
-
?
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- + H+
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
-
-
-
?
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- + H+
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
-
-
-
?
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- + H+
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
-
-
-
?
additional information
?
-
-
the purEK operon is regulated by the purR gene product
-
-
?
additional information
?
-
-
comparison of active site organization and reaction mechanism to purT-encoded glycinamide ribonucleotide formyltransferase, overview
-
-
?
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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 + 5-amino-1(5-phospho-D-ribosyl)imidazole + HCO3-
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
-
-
-
-
?
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- + H+
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
additional information
?
-
-
the purEK operon is regulated by the purR gene product
-
-
?
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- + H+
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
-
-
-
?
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- + H+
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
-
-
-
?
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- + H+
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
-
-
-
?
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- + H+
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
-
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1,1'-(imidazolidine-1,3-diyldimethanediyl)bis(1H-indole-2,3-dione)
-
class II inhibitor
1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)pentitol
-
noncompetitive, class III inhibitor
2-(2,3-dioxo-2,3-dihydro-1H-indol-1-yl)-N,N-diethylacetamide
-
noncompetitive, class II inhibitor
2-hydroxy-2-[(4-methyl-1,2,5-oxadiazol-3-yl)amino]-1H-indene-1,3(2H)-dione
-
class I inhibitor
5-bromo-1-([3-[(2,3-dioxo-2,3-dihydro-1H-indol-1-yl)methyl]imidazolidin-1-yl]methyl)-1H-indole-2,3-dione
-
-
-
5-[(2-hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)carbamoyl]-4-(trifluoromethyl)pyridin-2-olate
-
class I inhibitor
ethyl 1-[(2,3-dioxo-2,3-dihydro-1H-indol-1-yl)methyl]piperidine-4-carboxylate
-
class II inhibitor
ethyl 4-(2-[[(4-chlorophenyl)sulfonyl]methyl]-1,3-thiazol-4-yl)-1,2-oxazole-3-carboxylate
-
-
ethyl 4-(2-[[(4-chlorophenyl)sulfonyl]methyl]-1,3-thiazol-4-yl)-5-methyl-1,2-oxazole-3-carboxylate
-
class III inhibitor
N-(2-hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)-1,3-dimethyl-1H-pyrazole-5-carboxamide
-
-
N-(2-hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)-1-methyl-1H-pyrazole-5-carboxamide
-
class I inhibitor
N-(2-hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)-2-methyl-1,3-thiazole-4-carboxamide
-
class I inhibitor
N-(2-hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)-4-methoxythiophene-3-carboxamide
-
class I inhibitor
N-(2-hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)-6-methoxy-4-(trifluoromethyl)pyridine-3-carboxamide
-
-
N-(2-hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)-9-oxo-9H-fluorene-4-carboxamide
-
class I inhibitor
additional information
-
high-throughput screening for enzyme inhibitors, identification of inhibitor separated into three classes: class I contains compounds with an indenedione core. Class II contains an indolinedione group, and class III contains compounds that are structurally unrelated to other inhibitors in the group, overview
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
kinetics of recombinant mutant proteins, overview
-
0.0103
5-amino-1(5-phospho-D-ribosyl)imidazole
-
pH 8.0, 25°C, chimeric mutant with PurK activity
0.066
5-amino-1(5-phospho-D-ribosyl)imidazole
-
pH 8.0, 25°C, wild-type PurK
0.0139
5-amino-1-(5-phospho-D-ribosyl)imidazole
wild type enzyme, in 50 mM HEPES, 80 mM KCl, 20 mM MgCl2, at 22°C, pH not specified in the publication
0.0513
5-amino-1-(5-phospho-D-ribosyl)imidazole
mutant enzyme F78I, in 50 mM HEPES, 80 mM KCl, 20 mM MgCl2, at 22°C, pH not specified in the publication
0.103
5-amino-1-(5-phospho-D-ribosyl)imidazole
mutant enzyme F78W, in 50 mM HEPES, 80 mM KCl, 20 mM MgCl2, at 22°C, pH not specified in the publication
0.0432
ATP
wild type enzyme, in 50 mM HEPES, 80 mM KCl, 20 mM MgCl2, at 22°C, pH not specified in the publication
18.8
HCO3-
wild type enzyme, in 50 mM HEPES, 80 mM KCl, 20 mM MgCl2, at 22°C, pH not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
15.83
5-amino-1-(5-phospho-D-ribosyl)imidazole
mutant enzyme F78I, in 50 mM HEPES, 80 mM KCl, 20 mM MgCl2, at 22°C, pH not specified in the publication
18
5-amino-1-(5-phospho-D-ribosyl)imidazole
mutant enzyme F78W, in 50 mM HEPES, 80 mM KCl, 20 mM MgCl2, at 22°C, pH not specified in the publication
24.83
5-amino-1-(5-phospho-D-ribosyl)imidazole
wild type enzyme, in 50 mM HEPES, 80 mM KCl, 20 mM MgCl2, at 22°C, pH not specified in the publication
0.0013
HCO3-
mutant enzyme R271K, in 50 mM HEPES, pH 7.8, at 37°C
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
130
5-amino-1(5-phospho-D-ribosyl)imidazole
-
pH 8.0, 25°C, chimeric mutant with PurK activity
175
5-amino-1-(5-phospho-D-ribosyl)imidazole
mutant enzyme F78W, in 50 mM HEPES, 80 mM KCl, 20 mM MgCl2, at 22°C, pH not specified in the publication
308
5-amino-1-(5-phospho-D-ribosyl)imidazole
mutant enzyme F78I, in 50 mM HEPES, 80 mM KCl, 20 mM MgCl2, at 22°C, pH not specified in the publication
1783
5-amino-1-(5-phospho-D-ribosyl)imidazole
wild type enzyme, in 50 mM HEPES, 80 mM KCl, 20 mM MgCl2, at 22°C, pH not specified in the publication
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)pentitol
additional information
1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)pentitol
-
0.081 mM with fixed ATP and bicarbonate concentrations, 0.122 mM with fixed aminoimidazole ribonucleotide and bicarbonate concentrations
additional information
2-(2,3-dioxo-2,3-dihydro-1H-indol-1-yl)-N,N-diethylacetamide
-
0.029 mM with fixed ATP and bicarbonate concentrations, 0.04 mM with fixed aminoimidazole ribonucleotide and bicarbonate concentrations
additional information
ethyl 4-(2-[[(4-chlorophenyl)sulfonyl]methyl]-1,3-thiazol-4-yl)-1,2-oxazole-3-carboxylate
-
0.062 mM with fixed ATP and bicarbonate concentrations, 0.043 mM with fixed aminoimidazole ribonucleotide and bicarbonate concentrations
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.069
1,1'-(imidazolidine-1,3-diyldimethanediyl)bis(1H-indole-2,3-dione)
Escherichia coli
-
-
0.02
1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)pentitol
Escherichia coli
-
-
0.0023
2-hydroxy-2-[(4-methyl-1,2,5-oxadiazol-3-yl)amino]-1H-indene-1,3(2H)-dione
Escherichia coli
-
-
0.022
ethyl 1-[(2,3-dioxo-2,3-dihydro-1H-indol-1-yl)methyl]piperidine-4-carboxylate
Escherichia coli
-
-
0.01
ethyl 4-(2-[[(4-chlorophenyl)sulfonyl]methyl]-1,3-thiazol-4-yl)-1,2-oxazole-3-carboxylate
Escherichia coli
-
-
0.0078
N-(2-hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)-1,3-dimethyl-1H-pyrazole-5-carboxamide
Escherichia coli
-
-
0.0056
N-(2-hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)-2-methyl-1,3-thiazole-4-carboxamide
Escherichia coli
-
-
0.017
N-(2-hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)-4-methoxythiophene-3-carboxamide
Escherichia coli
-
-
0.017
N-(2-hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)-6-methoxy-4-(trifluoromethyl)pyridine-3-carboxamide
Escherichia coli
-
-
0.0087
N-(2-hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)-9-oxo-9H-fluorene-4-carboxamide
Escherichia coli
-
-
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strains, DH-5alpha and BL21(DE3), and purK- strain K-12 MG1655, gene purK
-
-
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
physiological function
-
key enzyme in microbial de novo purine biosynthesis
metabolism
-
the enzyme is involved in the de novo purine biosynthetic pathway
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homodimer
additional information
-
comparison of tertiary structure and active site organization to purT-encoded glycinamide ribonucleotide formyltransferase, PurK shows a three domain structure
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
structures with various combinations of ATP, ADP, Mg2+, hydrogencarbonate and aminoimidazole ribonucleotide in the active site. The binding involves interactions with the conserved residues Arg272, His274 and Lys348. The formation of a carboxyphosphate intermediate through ATP phosphoryl transfer is proposed, followed by carboxylation of AIR to give the product
Q81ZH7
hanging drop vapour diffusion of native enzyme, crystals of the native enzyme belong to space group C222(1) with unit cell dimensions of a = 93.4 A, b = 95.2 A and c = 120.6 A. Crystals of the enzyme/MgADP complex are grown by batch methods at room temperature with poly(ethylene glycol)8000 as precipitant. The crystals belong to the space group P1 with unit cell dimensions of a = 60.6 A, b = 92.1 A, c = 102.6 A, alpha = 66.1°, beta = 82.7° and gamma = 81.8°
hanging drop vapor diffusion method, using 0.1 M bis-Tris pH 6.5, 28% (w/v) polyethylene glycol monomethyl ether 2000
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D153A
E73A
K353A
R155A
R271K
the mutant shows almost no (1000fold) reducedactivity compared to the wild type enzyme and is more sensitive towards ATP substrate inhibition
Y152A
E73A
-
the mutant shows 2fold reduced activity compared to the wild type enzyme
-
F78I
the mutant shows strongly reduced catalytic efficiency compared to the wild type enzyme
F78W
the mutant shows strongly reduced catalytic efficiency compared to the wild type enzyme
F78I
-
the mutant shows strongly reduced catalytic efficiency compared to the wild type enzyme
-
F78W
-
the mutant shows strongly reduced catalytic efficiency compared to the wild type enzyme
-
additional information
-
generation of six recombinant hybrid proteins combining functional domains of PurK and PurT, glycinamide ribonucleotide formyltransferase, on the basis of structural and sequence alignments, overview. The mutant chimeras are functional and show activity with different substrates, overview
D153A
-
mutation without affecting substrate binding but critical role in catalysis, decrease in catalytic proficiency
E73A
-
mutation with affect on substrate binding, decrease in catalytic proficiency
E73A
the mutant shows 2fold reduced activity compared to the wild type enzyme
K353A
-
mutation without affecting substrate binding but critical role in catalysis, decrease in catalytic proficiency
R155A
-
mutation with affect on substrate binding, decrease in catalytic proficiency
Y152A
-
mutation with affect on substrate binding, decrease in catalytic proficiency
Y152A
the mutant shows 3fold reduced activity compared to the wild type enzyme
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni-NTA column chromatography and Superdex 200 gel filtration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
medicine
-
observed only in microorganisms, target for antimicrobial drug
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE