Information on EC 2.4.2.19 - nicotinate-nucleotide diphosphorylase (carboxylating)

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

EC NUMBER
COMMENTARY hide
2.4.2.19
-
RECOMMENDED NAME
GeneOntology No.
nicotinate-nucleotide diphosphorylase (carboxylating)
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
beta-nicotinate D-ribonucleotide + diphosphate + CO2 = pyridine-2,3-dicarboxylate + 5-phospho-alpha-D-ribose 1-diphosphate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pentosyl group transfer
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Metabolic pathways
-
-
NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde
-
-
NAD biosynthesis I (from aspartate)
-
-
NAD metabolism
-
-
Nicotinate and nicotinamide metabolism
-
-
nicotine biosynthesis
-
-
superpathway of nicotine biosynthesis
-
-
SYSTEMATIC NAME
IUBMB Comments
nicotinate-D-ribonucleotide:diphosphate phospho-alpha-D-ribosyltransferase (carboxylating)
The reaction is catalysed in the opposite direction. Since quinolinate is synthesized from L-tryptophan in eukaryotes, but from L-aspartate in some prokaryotes, this is the first NAD+ biosynthesis enzyme shared by both eukaryotes and prokaryotes [3].
CAS REGISTRY NUMBER
COMMENTARY hide
37277-74-0
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
DOB1 and other phthalate-degrading strains have two dissimilar genes for this enzyme, while non-phthalate-degrading strains have only a single gene
-
-
Manually annotated by BRENDA team
strain PsJN
-
-
Manually annotated by BRENDA team
strain PsJN
-
-
Manually annotated by BRENDA team
-
Uniprot
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
serotype M6
UniProt
Manually annotated by BRENDA team
serotype M6
UniProt
Manually annotated by BRENDA team
strain MSB8, gene TM1645
SwissProt
Manually annotated by BRENDA team
i.e. Vigna radiata
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
nicotinate + 5-phospho-alpha-D-ribose 1-diphosphate + ATP + H2O
beta-nicotinate D-ribonucleotide + diphosphate + ADP + phosphate
show the reaction diagram
pyridine-2,3-dicarboxylate + 5-phospho-alpha-D-ribose 1-diphosphate
nicotinate D-ribonucleotide + diphosphate + CO2
show the reaction diagram
pyridine-2,3-dicarboxylate + 5-phospho-alpha-D-ribose 1-diphosphate + H+
beta-nicotinate D-ribonucleotide + diphosphate + CO2
show the reaction diagram
quinolinic acid + 5-phospho-alpha-D-ribose 1-diphosphate
nicotinic acid mononucleotide + diphosphate + CO2
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
pyridine-2,3-dicarboxylate + 5-phospho-alpha-D-ribose 1-diphosphate
nicotinate D-ribonucleotide + diphosphate + CO2
show the reaction diagram
pyridine-2,3-dicarboxylate + 5-phospho-alpha-D-ribose 1-diphosphate + H+
beta-nicotinate D-ribonucleotide + diphosphate + CO2
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
NAD+
-
0.1 mM, 75% inhibition
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Cd2+
-
can partially replace Mg2+
Co2+
-
can partially replace Mg2+
K+
-
monovalent cation required, K+, Li+ or NH4+ markedly stimulate
Li+
-
monovalent cation required, K+, Li+ or NH4+ markedly stimulate
NH4+
-
monovalent cation required, K+, Li+ or NH4+ markedly stimulate
Zn2+
-
can partially replace Mg2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-Hydroxynicotinate
-
50% at 0.01 M
2-oxoglutarate
5-phospho-alpha-D-ribose 1-diphosphate
-
substrate inhibition, mixed inhibition (competitive and non-competitive) above 0.3 mM 5-phospho-alpha-D-ribose 1-diphosphate
5-phosphoribosyl-1-diphosphate
acetic acid
-
26% inhibition
Ag+
-
1 mM, complete inhibition
AMP
-
2 mM, 7% inhibition
aspartic acid
Ba2+
-
1 mM, 38.1% inhibition
Ca2+
-
1 mM, 34.9% inhibition
Citric acid
Cr3+
-
1 mM, 46.4% inhibition
D-fructose-1,6-diphosphate
competitive with respect to 5-phosphoribosyl-1-diphosphate and noncompetitive with respect to quinolinate
diphosphate
noncompetitive with respect to both 5-phosphoribosyl-1-diphosphate and quinolinate
dipicolinic acid
-
1 mM, 24% inhibition
dithiobis(2-nitrobenzoic acid)
-
10 mM, 88.7% inhibition
dTDP
-
1 mM, 14% inhibition
dTTP
-
1 mM, 29% inhibition
formic acid
-
1 mM, 54% inhibition
Fumaric acid
GDP
-
2 mM, 29% inhibition
glycerol
IDP
-
2 mM, 29% inhibition
IMP
-
2 mM, 6% inhibition
isocinchomeric acid
-
1 mM, 15% inhibition
L-Glutamic acid
L-Malic acid
Lactic acid
-
1 mM, 29% inhibition
lutidinic acid
-
1 mM, 17% inhibition
Maleic acid
methyl-3-amidopyridine-2-carboxylate
-
-
methyl-3-cyanopyridine 2-carboxylate
-
-
Mg2+
-
1 mM, 7.7% inhibition
Mn2+
-
1 mM, 80.3% inhibition
Monoiodoacetic acid
Na4P2O7
-
3 mM, complete inhibition
NAD+
-
19% inhibition at 1 mM, 15% inhibition at 10 mM
NEM
-
5 mM, 86% inhibition
nicotinate mononucleotide
oxaloacetic acid
PCMB
-
0.05 mM, complete inhibition
Phthalic acid
Picolinic acid
-
-
Sr2+
-
47.6% inhibition
succinic acid
Tris
-
-
UDP
-
2 mM, 32% inhibition
additional information
-
nicotinic acid and nicotinamide inhibit growth of roots
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
glycerol
-
glycerol markedly activates enzyme activity at pH 6.1 and pH 6.5, inhibition above pH 7.0, inhibition is strongest at pH 9.0
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0156 - 4.12
5-phospho-alpha-D-ribose 1-diphosphate
0.01 - 0.151
nicotinic acid
0.0051 - 0.133
quinolinate
0.0216 - 1.478
quinolinic acid
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.048
nicotinic acid
Salmonella enterica subsp. enterica serovar Typhimurium
-
mutant K185A, at 25C
6
pyridine-2,3-dicarboxylate
Streptococcus pyogenes
Q5XBL7
37C, pH 7.5
0.00024 - 1.6
quinolinic acid
additional information
5-phospho-alpha-D-ribose 1-diphosphate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00004 - 18
5-phospho-alpha-D-ribose 1-diphosphate
0.32
nicotinic acid
Salmonella enterica subsp. enterica serovar Typhimurium
-
mutant K185A, at 25C
1282
0.0011 - 52
quinolinic acid
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.05 - 2.2
5-phosphoribosyl-1-diphosphate
0.063 - 0.0838
nicotinate mononucleotide
0.0014 - 0.17
Phthalic acid
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.0006
-
wild-type with nicotinic acid at 1 mM and 2 mM 5-phospho-alpha-D-ribose 1-diphosphate
0.0133
-
enzyme from liver
0.0187
-
enzyme from brain
0.0227 - 0.0919
-
enzyme from kidney
0.05169
-
-
0.0517
-
-
0.07
-
mutant R152A with nicotinic acid at 1 mM and 2 mM 5-phospho-alpha-D-ribose 1-diphosphate
0.073
-
-
0.09
-
wild-type, 0.1 mM 5-phospho-alpha-D-ribose 1-diphosphate, UV-based assay measuring nicotinic acid mononucleotide formation at 266 nm, 30 min, 37C, same order of magnitude as bacterial enzymes, 100% relative activity
0.091
-
-
0.1
-
mutant R152A with quinolinic acid at 1 mM and 2 mM 5-phospho-alpha-D-ribose 1-diphosphate
1.2
-
wild-type with quinolinic acid at 1 mM and 2 mM 5-phospho-alpha-D-ribose 1-diphosphate
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6
-
in presence of 1 mM 5-phospho-alpha-D-ribose 1-diphosphate, enzyme from liver
6.2
-
-
6.5 - 7.7
-
-
9
-
in presence of 0.4 mM 5-phospho-alpha-D-ribose 1-diphosphate, enzyme from kidney and liver
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.2 - 7.8
-
half maximal activity at pH 5.2 and pH 7.8
6.4 - 7.3
-
pH 6.4: about 50% of maximal activity, pH 7.3: about 55% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.1
sequence calculation, residues 1-273
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
embryonic axes, high enzyme activity
Manually annotated by BRENDA team
-
endosperm of etiolated seedlings
Manually annotated by BRENDA team
additional information
-
nicotinic acid metabolism and content of trigonelline in different tissues of the seeds and seedlings and during differentiation
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Burkholderia pseudomallei (strain 1710b)
Ehrlichia chaffeensis (strain ATCC CRL-10679 / Arkansas)
Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)
Helicobacter pylori (strain ATCC 700392 / 26695)
Helicobacter pylori (strain ATCC 700392 / 26695)
Helicobacter pylori (strain ATCC 700392 / 26695)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
31700
calculated from amino acid sequence
68000
-
gel filtration
70000
gel filtration
160000
167000
-
sucrose density gradient centrifugation
170000
-
gel filtration
172000
-
sedimetation velocity method
173000
-
gel filtration
178000
-
calculation from sedimentation and ultracentrifugation data
202000
-
equilibrium sedimentation
210000
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
homohexamer
octamer
-
8 * 27500, SDS-PAGE
pentamer
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
glycoprotein
-
enzyme contains 1% mannose
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure of Hp-QAPRTase with bound quinolinic acid, nicotinic acid mononucleotide, and phthalic acid. Hp-QAPRTase crystals are grown at 20C using the hanging drop vapor diffusion method
hanging-drop vapor-diffusion method
-
hanging-drop vapour-diffusion method, PEG MME 2K
-
PDB code: 2jbm (apo-hQPRTase), alpha/beta barrel fold (12 beta strands + 11 alpha helices) with N-terminal domain (residues 1-112, 279-291) and C-terminal domain (residues 113-278), similar to bacterial QPRTases (PDB: 1x1o), active site at alpha/beta open sandwich structure that faces an alpha/beta barrel of the adjacent subunit harbouring the quinolinic acid binding site (Arg102, Arg138, Arg161, Lys139, Lys171, pocket at the centre of the barrel), space group P2(1)2(1)2(1), unit-cell parameters: a = 111.5 A, b = 179.5 A, c = 194.7 A, 12 monomers in asymmetric unit arranged as 2 hexamers of D3 symmetry, sitting-drop vapour diffusion: 5 days, 20C, 2 microlitre protein solution (10 mg/ml, pH7.5) + 2 microlitre precipitant (0.6 M potassium/sodium tartrate, 0.1 M sodium HEPES pH7.6), resolution of 2 A, phase determination using multiple wavelength anomalous diffraction on crystals of the Se-Met variant
-
hangig-drop vapor diffusion method, X-ray crystal structure of the apoenzyme is determined by multiple isomorphous replacement at 2.4 A resolution, complex with quinolinate, phthalate, nicotinate mononucleotideand ternary complex with phthalate and a substrate analog 5-phosphoribosyl-1-(beta-methylene)diphosphate
-
apo, quinolinate-bound, 5-phospho-alpha-D-ribose 1-diphosphate-bound, and phthalate-bound forms. Crystallized at room temperature by the hanging drop vapor diffusion method. Both apo and holo crystals belong to space group R32 (alpha = 90, beta = 90, and gamma = 120). One molecule per asymmetric unit except in QAPRTase holophthalate crystals where two molecules are found. The unit cell dimensions are: a = b = 154.9 A and c = 68.9 A (apo), a = b = 154.8 A and c = 68.6 A (holoquinolinate), a = b = 154.9 A and c = 70.6 A (holo-5-phospho-alpha-D-ribose 1-diphosphate), a = b = 155.5 A and c = 121.1 A (holophthalate), a = b = 154.7 A and c = 69.3 A (holophthalate-5-phospho-alpha-D-ribose 1-diphosphate)
hanging-drop vapor-diffusion method, determination of crystal structure of the enzyme with bound quinolinate to 2.8 A resolution and with bound nicotinic acid mononucleotide
-
hanging-drop vapour-diffusion method, PEG 8000
-
purified recombinant enzyme, hanging drop vapour diffusion method, 10 mg/ml protein, crystallization solution contains 10% PEG 6000, and 0.1 M MES, pH 6.0, X-ray diffraction structure determination and analysis at 2.5 A resolution, molecular replacement, model construction
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3 - 3.5
-
37C, denatured abruptly
638028
4.5 - 9.5
-
37C, 30 min, completely stable
638028
5.5 - 10
-
-
638015
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
55
-
10 min, 48% loss of activity
80
-
3 min, 50% loss of activity
additional information
-
quinolinate at 0.8 mM gives 50% protection against heat inactivation. 22% inhibition in presence of quinolinate
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, enzyme in treated extract, stable
-
-90C, stable for several months in 0.05 M potassium phosphate buffer, pH 7.0, 50% sucrose w/v and 0.01 M dithiothreitol
-
0-4C, crystalline enzyme is stable for at least 2 years
-
4C, stable for 1 month
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate precipitation, dye ligand chromatography (Blue-Sepharose), ion exchange chromatography
-
by anion exchange chromatography
from porcine kidney, ammonium sulfate fractionation, ion exchange chromatography (DEAE), gel filtration
-
immobilized metal ion affinity chromatography (Ni2+), gel filtration
-
mutants purified by gel filtration, to homogeneity
-
mutants purified to homogeneity in 250 mg yield from a 6 liter culture, by gel filtration
-
nickel affinity chromatography, TEV protease cleavage followed by nickel affinity chromatography, gel filtration, selenomethionine variant of hQPRTase purified in presence of 5 mM beta-mercaptoethanol
-
recombinant enzyme
-
recombinant N-terminally His-tagged enzyme from Escherichia coli b nickel affinity chromatography
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli as glutathione S-transferase fusion protein
-
expressed in Escherichia coli BL21(DE3)-RIPL Codon Plus
-
expressed in Escherichia coli TH265 (nadC mutant)(complementation approach); expressed in Escherichia coli TH265 (nadC mutant)(complementation approach)
expression in Escherichia coli
gene TM1645, expression of N-terminally His-tagged enzyme in Escherichia coli
His-tagged protein expressed in Escherichia coli C41 (DE3)
-
in pEHISTEV (pBS-hQPRT as template) for expression in Escherichia coli BL21(DE3) or mutagenesis, expression with N-terminal hexa-His tag and TEV protease cleavage site, two extra N-terminal residues (Gly, Ala) remain after removal of hexa-His tag
-
into plasmid pTYB12 and expressed in Escherichia coli BL21
nadC coding sequence cloned into the pRSETC expression vector, overexpressed in Escherichia coli nadC-deleted host strain ZB100
-
overexpression in Escherichia coli
-
subcloned into a T7-based expression system
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K139A
-
inactive, K139 is part of quinolinic acid binding site
K139S
-
inactive, K139 is part of quinolinic acid binding site
K171A
-
inactive, K171 is part of quinolinic acid binding site
K171S
-
inactive, K171 is part of quinolinic acid binding site
R102A
-
10% remaining activity, R102 is part of quinolinic acid binding site, denotes from the other subunit in the canonical dimer
R102Q
-
10% remaining activity, R102 is part of quinolinic acid binding site, denotes from the other subunit in the canonical dimer
R138Q
-
inactive, R138 is part of quinolinic acid binding site
R161A
-
20% remaining activity, R161 is part of quinolinic acid binding site and important for substrate binding
R161Q
-
inactive, R161 is part of quinolinic acid binding site
D235A
-
does not affect ligand binding or catalysis, KD value for quinolinic acid is similar to wild-type, increases KD value for 5-phospho-alpha-D-ribose 1-diphosphate by 2fold
E214A
-
increases KD value for quinolinic acid by 2fold and for 5-phospho-alpha-D-ribose 1-diphosphate by 15fold, causes at least a 4000fold reduction in kcat. Presence of benzene-1,2-dicarboxylic acid results in 3.4fold tightening of 5-phospho-alpha-D-ribose 1-diphosphate binding
E214D
-
KD value for quinolinic acid is similar to wild-type, increases KD value for 5-phospho-alpha-D-ribose 1-diphosphate by 10fold. Presence of benzene-1,2-dicarboxylic acid results in 6fold tightening of 5-phospho-alpha-D-ribose 1-diphosphate binding
E214Q
-
increases KD value for quinolinic acid by 2fold and for 5-phospho-alpha-D-ribose 1-diphosphate by 2fold, has only modest effects on ligand binding and catalysis, wild-type-like pH profile. Presence of benzene-1,2-dicarboxylic acid results in 2fold tightening of 5-phospho-alpha-D-ribose 1-diphosphate binding
K153A
-
inactive enzyme, kcat value decreases by more than 4000fold, is able to bind quinolinic acid with a KD value 2fold higher than that of wild-type
K185A
-
kcat value is reduced by 625fold, and binding affinity of quinolinic acid and 5-phospho-alpha-D-ribose 1-diphosphate to the enzyme decreases. Displays 83fold increase in activity toward the normally inactive quinolinic acid analogue, nicotinic acid. Displays a 300fold higher kcat/Km for nicotinic acid over the natural substrate quinolinic acid
K284A
-
KD value for quinolinic acid is similar to wild-type, decreases kcat by 30fold and increases Km and KD values for 5-phospho-alpha-D-ribose 1-diphosphate by 80fold and at least 20fold, respectively
R118A
-
results in 5000fold decrease in kcat value and a decrease in the binding affinity of quinolinic acid and 5-phospho-alpha-D-ribose 1-diphosphate to mutant R152A. Equimolar mixtures of mutant R118A with inactive or virtually inactive mutants produce approximately 50% of the enzymatic activity of wild-type
R152A
-
kcat value is reduced by 33fold, and binding affinity of quinolinic acid and 5-phospho-alpha-D-ribose 1-diphosphate to the enzyme decreases. Displays 116fold increase in activity toward the normally inactive quinolinic acid analogue, nicotinic acid
additional information
-
mutants can use 6-aminonicotinic acid as substrate, whereas 2,4-pyridinedicarboxylic acid, 2,5-pyridinedicarboxylic acid, 2,6-pyridinedicarboxylic acid, 3,4-pyridinedicarboxylic acid, 3,5-pyridinedicarboxylic acid, nicotinamide and pyridine-4-carboxylic acid are not utilized by the mutant enzymes
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