Information on EC 2.7.1.19 - phosphoribulokinase

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

EC NUMBER
COMMENTARY hide
2.7.1.19
-
RECOMMENDED NAME
GeneOntology No.
phosphoribulokinase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + D-ribulose 5-phosphate = ADP + D-ribulose 1,5-bisphosphate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phospho group transfer
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Calvin-Benson-Bassham cycle
-
-
Carbon fixation in photosynthetic organisms
-
-
Metabolic pathways
-
-
Microbial metabolism in diverse environments
-
-
Rubisco shunt
-
-
photosynthesis
-
-
SYSTEMATIC NAME
IUBMB Comments
ATP:D-ribulose-5-phosphate 1-phosphotransferase
-
CAS REGISTRY NUMBER
COMMENTARY hide
9030-60-8
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Pseudomonas facilis
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
; strain 18; strain 19
-
-
Manually annotated by BRENDA team
; strain 18
-
-
Manually annotated by BRENDA team
; strain 19
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
Uniprot
Manually annotated by BRENDA team
Chromatium sp.
strain D
-
-
Manually annotated by BRENDA team
strain D
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
cultivar 108-F
-
-
Manually annotated by BRENDA team
-
Uniprot
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
no activity in Roseobacter denitrificans OCh 114
-
-
-
Manually annotated by BRENDA team
-
Uniprot
Manually annotated by BRENDA team
strain 926-1
Uniprot
Manually annotated by BRENDA team
strain 926-1
Uniprot
Manually annotated by BRENDA team
variant Little Marvel
-
-
Manually annotated by BRENDA team
green unicellar alga
-
-
Manually annotated by BRENDA team
strain 127.79
Uniprot
Manually annotated by BRENDA team
strain 127.79
Uniprot
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain 01150
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
green alga
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
physiological function
the enzyme strengthens the interaction between glyceraldehyde-3-phosphate dehydrogenase and chloroplast protein 12 within the supra-molecular complex
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + D-ribulose 5-phosphate
ADP + D-ribulose 1,5-bisphosphate
show the reaction diagram
D-fructose 6-phosphate + ATP
?
show the reaction diagram
-
3.6% of ribulose 5-phosphate activity
-
-
?
D-ribose 5-phosphate + ATP
D-ribose 1,5-diphosphate + ADP
show the reaction diagram
-
-
PRK activity of multienzyme complexes is higher with D-ribose-5-phosphate and ATP than in the presence of D-ribulose 5-phosphate
-
?
D-ribulose 5-phosphate + ATP
D-ribulose 1,5-diphosphate + ADP
show the reaction diagram
D-ribulose 5-phosphate + GTP
D-ribulose 1,5-diphosphate + GDP
show the reaction diagram
-
-
-
-
?
D-ribulose 5-phosphate + trinitrophenyl-ATP
D-ribulose 1,5-diphosphate + trinitrophenyl-ADP
show the reaction diagram
D-ribulose 5-phosphate + UTP
D-ribulose 1,5-diphosphate + UDP
show the reaction diagram
-
-
-
-
?
sedoheptulose 7-phosphate + ATP
?
show the reaction diagram
-
2.5% of ribulose 5-phosphate activity
-
-
?
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 + D-ribulose 5-phosphate
ADP + D-ribulose 1,5-bisphosphate
show the reaction diagram
D-ribulose 5-phosphate + ATP
D-ribulose 1,5-diphosphate + ADP
show the reaction diagram
additional information
?
-
-
association between binding protein CP12 and phosphoribulokinase (EC 2.7.1.19), glyceraldehyde 3-phosphate dehydrogenase (EC 1.2.1.13) and aldolase. The dissociation constant between CP12 and fructose 1,6-bisphosphate (EC 4.1.2.13) aldolase is 0.00048 mM and thus corroborates an interaction between CP12 and aldolase. The dissociation constant between aldolase and the phosphoribulokinase/lyceraldehyde 3-phosphate dehydrogenase/CP12 complex is 55 mM
-
-
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
EDTA
-
activation
K+
-
required
phosphate
-
activation
additional information
-
not activated by Ni2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3-phosphoglycerate
-
74% inhibition at 6 mM and pH 7.2
5,5'-dithiobis(2-nitrobenzoic acid)
DTNB, Ellmans reagent, almost complete inhibition at 0.0045 mM
6-phospho-D-gluconate
6-phosphogluconate
-
competitive inhibitor, 78% residual activity at 1 mM
chloroplast protein 12
-
cystine
-
oxidized form, inhibition almost completely reversible by addition of reduced dithiothreitol
D-Ribulose 1,5-diphosphate
daphnetin
-
i.e. 7,8-dihydroxycoumarin
diethyl dicarbonate
-
27% residual activity at 0.04 mM
dithiobis-(2-nitrobenzoic acid)
-
complete inactivation, 3 mM ATP protects
dithiothreitol
DL-glyceraldehyde
-
non competitive, 10 mM
glutathione
H2O2
-
complete inactivation, 3 mM ATP protects
iodoacetate
-
-
L-aspartate
-
competitive, 1 mM
L-malate
-
competitive, 1 mM
p-chloromercuribenzoate
-
-
phosphoenolpyruvate
pyridoxal 5'-phosphate
regulatory protein CP12
-
forming under oxidizing conditions a supramolecular complex (2 phosphoribulokinase dimers + 2 glyceraldehyde-3-phosphate dehydrogenase tetramers + 4 CP12 monomers)
-
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-mercaptoethanol
-
above 2 mM
alpha-glycerophosphate
-
activation
D-glucose 1-phosphate
-
activation
D-glucose 6-phosphate
D-ribose 5-phosphate
-
11% increase of activity
dithiothreitol
glyceraldehyde 3-phosphate
-
activation
glycine
-
activation
reduced glutathione
thioredoxin
additional information
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.062 - 1.42
ATP
0.048 - 11
D-ribulose 5-phosphate
additional information
additional information
-
kinetics
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.2 - 19.8
6-phospho-D-gluconate
0.32 - 10
D-ribulose 1,5-bisphosphate
19 - 20
DL-glyceraldehyde
-
pH 7.9, 20C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.018
-
crude extract
0.029
-
crude extract
0.031
-
crude extract
0.04
-
crude extract
0.068
-
crude extract
0.069
-
crude extract
0.074
-
crude extract
0.075
-
crude extract
0.081
-
crude extract
0.097
-
crude extract
0.176
-
crude extract
0.198
-
crude extract
0.306
-
crude extract
0.331
-
crude extract
0.563
-
crude extract
0.62
-
crude extract
1.831
-
crude extract
3.895
-
crude extract
15.17
-
after activation by reduced thioredoxin
148
-
high MW form
204
-
low MW form
300
purified enzyme, pH 8
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.6
-
presence of NADH
8 - 8.4
-
-
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 9.2
-
no activity above and below
7 - 8.2
-
less than 50% of maximal activity above and below
8.2
-
50% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.1
-
non-denaturatung isoelectric focusing
5.75
-
calculated from amino acid sequence
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
less expressed in flower, and little or not expressed in root and silique
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
18800
-
x * 18800 + x * 57500, SDS-PAGE
26000
-
1 * 43000 + 1 * 26000, SDS-PAGE in presence of 2-mercaptoethanol
32000
-
8 * 32000
36000
-
6 * 36000, SDS-PAGE
38000
x * 38000 Da, Western-blot analysis
38500
-
x * 38500, calculated from sequence of cDNA, SDS-PAGE
39000
-
8 * 39000 + 4 * 42000, high MW form, SDS-PAGE
42000
-
2 * 42000, low MW form, SDS-PAGE; 8 * 39000 + 4 * 42000, high MW form, SDS-PAGE
43000
-
1 * 43000 + 1 * 26000, SDS-PAGE in presence of 2-mercaptoethanol
47000
-
1 * 48000 + 1 * 47000 + 1 * 41000 + 1 * 33000, SDS-PAGE
53000
-
4 * 53000, SDS-PAGE
57500
-
x * 18800 + x * 57500, SDS-PAGE
72000
-
gel filtration
82800 - 83000
90000
-
non-denaturing gel electrophoresis
97000
-
isolated enzyme, reduced form, gel filtration
110000
-
isolated enzyme, oxidized form, gel filtration
178000
-
gel filtration
180000
-
gel filtration
200000 - 230000
-
sucrose densitiy gradient centrifugation, gel filtration, PAGE
230000
237000
248000
-
sucrose density gradient centrifugation
250000
-
native enzyme
252000 - 256000
-
sedimentation equilibrium centrifugation, gel filtration
470000
-
high MW form, low speed sedimentation equilibrium centrifugation
520000
-
sucrose density gradient centrifugation
640000
-
glyceraldehyde-3-phosphate dehydrogenase/CP12/phosphoribulokinase complex, gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dodecamer
-
8 * 39000 + 4 * 42000, high MW form, SDS-PAGE
hexamer
multimer
octamer
tetramer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
sitting drop vapor diffusion method with NH4H2PO4 as precipitating agent
-
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10
stable for at least 2 h
25
unstable when assay is performed at 25C
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
unstable to repeated freezing/thawing
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-10C, stable
-
-20C, 50 mM Tris-HCl buffer, pH 8.0, 1 mM 2-mercaptoethanol
-
-20C, no loss of activity for 4 weeks
-
-80C, 10 mM bicine-KOH buffer, pH 7.8, 100 mM KCl, 5 mM dithiothreitol, several months
-
-80C, 100 mM Tris buffer, pH 8.0, 0.5 mM dithiothreitol, 10% v/v glycerol
-
-80C, N2-atmosphere, 50 mM bicine-KOH, 10 mM potassium phosphate, 10 mM dithiothreitol, 1 mM EDTA, 10% v/v glycerol, 2 months
-
0-4C, 100 mM imidazole-HCl buffer, pH 7.0, 10 mM MgCl2, 1 mM EDTA, 1 mM dithioerythritol, 3 months
-
0-4C, no significant loss of activity after 1 month
-
0-4C, pH 6.8, dithiothreitol, EDTA, 4 weeks
-
4C, 0.02 M triethanolamine-HCl buffer, pH 7.6, 0.5 mM EDTA, 0.5 mM dithiothreitol, 4 months
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
from chloroplasts
glyceraldehyde-3-phosphate dehydrogenase/CP12/phosphoribulokinase complex
-
homogeneity
purification as a complex with alkaline fructose 1,6-bisphosphatase
-
Q Sepharose chromatography
-
recombinant enzyme
Sephadex G-50 column gel filtration and DEAE cellulose column chromatography
-
wild-type and mutant enzymes
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
expressed in Escherichia coli Rosetta BL21(DE3) cells
expressed in Escherichia coli strain BL21(DE3)
-
wild-type and mutants
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
cold acclimation does not alter the level of phosphoribulokinase mRNA or its enzyme activity
-
maximum expression of prk transcript is detected 6 h postillumination with 78.6fold increases. 2 h into the 12 h dark cycle, prk transcript level is still elevated 31.2fold
-
prk transcript levels decrease upon illumination (13.4fold by 2 h post-illumination) and by 1.5fold after 2 h dark. Enzyme activity decreases with increasing starvation time, though activity is still measureable after 6 months
-
the enzyme is downpregulated by dithiothreitol
the enzyme is downregulated by NADPH
the enzyme is not influenced by dithiothreitol
the enzyme is not influenced by dithiothreitol and NADPH
the enzyme is not influenced by dithiothreitol and NADPH; the enzyme is not influenced by NADPH
the enzyme is not influenced by NADPH
the enzyme is not influenced by NADPH and dithiothreitol
-
the enzyme is strongly upregulated by dithiothreitol
the enzyme is upregulated by dithiothreitol
the enzyme is upregulated by NADPH
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D169A
-
fully functional substrate binding sites
D42A
-
fully functional substrate binding sites
H100A
-
reduced activity
H100N
-
reduced activity
H100Q
-
reduced activity
H45N
-
similar to wild type enzyme
K165C
-
reduced catalytic activity
K165M
-
reduced catalytic activity, insensitive to inactivation by pyridoxal 5'-phosphate
K53M
-
sensitive to inactivation by pyridoxal 5'-phosphate
R168Q
-
300fold decrease in catalytic efficiency, 50fold increased Km for D-ribulose 5-phosphate
R173Q
-
100fold increased Km for D-ribulose 5-phosphate
R186Q
-
decreased Km for D-ribulose 5-phosphate
R187Q
-
increased Km for D-ribulose 5-phosphate
S14A
-
decreased Vmax by 40fold
S19A
-
ability to form complexes with Mg-ATP2-, decreased Vmax, increased Km for D-ribulose 5-phosphate
T18A
-
ability to form complexes with Mg-ATP2-, increased Km for D-ribulose 5-phosphate, decreased Vmax
T20A
-
ability to form complexes with Mg-ATP2-
Y98L
-
reduced activity
C16S/C244S/C250S
-
triple mutant with altered oxidation-reduction midpoint potential as wild-type enzyme
C244S/C250S
-
double mutant with same oxidation-reduction midpoint potential as wild-type enzyme
additional information
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