Information on EC 6.3.4.18 - 5-(carboxyamino)imidazole ribonucleotide synthase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea

EC NUMBER
COMMENTARY hide
6.3.4.18
-
RECOMMENDED NAME
GeneOntology No.
5-(carboxyamino)imidazole ribonucleotide synthase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- = ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
show the reaction diagram
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-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
carboxylation
decarboxylation
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biosynthesis of antibiotics
-
-
Biosynthesis of secondary metabolites
-
-
inosine-5'-phosphate biosynthesis I
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inosine-5'-phosphate biosynthesis III
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Metabolic pathways
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Purine metabolism
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purine metabolism
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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.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
ATCC 6872
-
-
Manually annotated by BRENDA team
NK6051
-
-
Manually annotated by BRENDA team
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A6QFS4
UniProt
Manually annotated by BRENDA team
-
A6QFS4
UniProt
Manually annotated by BRENDA team
DSM1617
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
physiological function
-
key enzyme in microbial de novo purine biosynthesis
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
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
show the reaction diagram
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3-
ADP + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole + phosphate
show the reaction diagram
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3-
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
show the reaction diagram
-
-
-
-
?
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- + H+
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
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
show the reaction diagram
-
-
-
-
?
ATP + 5-amino-1-(5-phospho-D-ribosyl)imidazole + HCO3- + H+
ADP + phosphate + 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
show the reaction diagram
additional information
?
-
-
the purEK operon is regulated by the purR gene product
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-
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,1'-(imidazolidine-1,3-diyldimethanediyl)bis(1H-indole-2,3-dione)
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; 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
1-[(4-methylpiperazin-1-yl)methyl]-1H-indole-2,3-dione
-
; class II 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-(trifluoromethoxy)-1H-indole-2,3-dione
-
; class II inhibitor
5-bromo-1-(morpholin-4-ylmethyl)-1H-indole-2,3-dione
-
; class II 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
ATP
substrate inhibition
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
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; 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
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class I inhibitor
N-(2-hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)-2-methyl-1,3-thiazole-4-carboxamide
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; class I inhibitor
N-(2-hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)-4-methoxythiophene-3-carboxamide
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; class I inhibitor
N-(2-hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)-6-methoxy-4-(trifluoromethyl)pyridine-3-carboxamide
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N-(2-hydroxy-1,3-dioxo-2,3-dihydro-1H-inden-2-yl)-9-oxo-9H-fluorene-4-carboxamide
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; class I inhibitor
riboflavin
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-
additional information
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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 hide
LITERATURE
IMAGE
0.0103 - 0.066
5-amino-1(5-phospho-D-ribosyl)imidazole
0.0139 - 0.46
5-amino-1-(5-phospho-D-ribosyl)imidazole
0.0068 - 0.048
ATP
2.8 - 80
HCO3-
additional information
additional information
-
kinetics of recombinant mutant proteins, overview
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
15.83 - 24.83
5-amino-1-(5-phospho-D-ribosyl)imidazole
0.87 - 5.9
ATP
0.0013 - 0.25
HCO3-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
120 - 130
5-amino-1(5-phospho-D-ribosyl)imidazole
40162
0.67 - 5500
5-amino-1-(5-phospho-D-ribosyl)imidazole
5283
84 - 89
ATP
4
0.017 - 16.7
HCO3-
195
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.2 - 3.3
ATP
additional information
1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)pentitol
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.069
1,1'-(imidazolidine-1,3-diyldimethanediyl)bis(1H-indole-2,3-dione)
Escherichia coli
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-
0.02
1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)pentitol
Escherichia coli
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-
0.037
1-[(4-methylpiperazin-1-yl)methyl]-1H-indole-2,3-dione
Escherichia coli
-
-
0.0105
2-(2,3-dioxo-2,3-dihydro-1H-indol-1-yl)-N,N-diethylacetamide
Escherichia coli
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-
0.0023
2-hydroxy-2-[(4-methyl-1,2,5-oxadiazol-3-yl)amino]-1H-indene-1,3(2H)-dione
Escherichia coli
-
-
0.019
5-(trifluoromethoxy)-1H-indole-2,3-dione
Escherichia coli
-
-
0.023
5-bromo-1-(morpholin-4-ylmethyl)-1H-indole-2,3-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 hide
LITERATURE
0.23
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wild-type PurK, ADP formation
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8
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assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22
-
assay at room temperature
25
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assay at
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)
Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)
Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)
Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)
Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)
Staphylococcus aureus (strain Newman)
Staphylococcus aureus (strain Newman)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
39000
-
2 * 39000, SDS-PAGE
78000
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sucrose density gradient ultracentrifugation
79000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
-
2 * 39000, SDS-PAGE
homodimer
additional information
-
comparison of tertiary structure and active site organization to purT-encoded glycinamide ribonucleotide formyltransferase, PurK shows a three domain structure
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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
A6QFS4
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
HisPur cobalt resin column chromatography
Ni-NTA column chromatography and Superdex 200 gel filtration
A6QFS4
standard methods with nickel nitrilotiacetic acid resin
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21 Star (DE3) cells
A6QFS4
expressed in Escherichia coli BL21(DE3) pLysS cells
expression in Escherichia coli HMS174 cells
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
R271K
the mutant shows almost no (1000fold) reducedactivity compared to the wild type enzyme and is more sensitive towards ATP substrate inhibition
Y152F
the mutant shows wild type activity
E73A
-
the mutant shows 2fold reduced activity compared to the wild type enzyme
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H273A
-
inactive
-
K353A
-
inactive
-
R271A
-
inactive
-
Y152F
-
the mutant shows wild type activity
-
F78I
A6QFS4
the mutant shows strongly reduced catalytic efficiency compared to the wild type enzyme
F78W
A6QFS4
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
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F78W
-
the mutant shows strongly reduced catalytic efficiency compared to the wild type enzyme
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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
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
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