Information on EC 2.7.1.15 - ribokinase

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

EC NUMBER
COMMENTARY hide
2.7.1.15
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RECOMMENDED NAME
GeneOntology No.
ribokinase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + D-ribose = ADP + D-ribose 5-phosphate
show the reaction diagram
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-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phospho group transfer
Phosphorylation
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
degradation of pentoses
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Pentose phosphate pathway
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ribose degradation
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SYSTEMATIC NAME
IUBMB Comments
ATP:D-ribose 5-phosphotransferase
2-Deoxy-D-ribose can also act as acceptor.
CAS REGISTRY NUMBER
COMMENTARY hide
9026-84-0
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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
ATP + 2-deoxy-D-ribitol
ADP + 2-deoxy-D-ribitol 5-phosphate
show the reaction diagram
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41% of the activity with 2-deoxy-D-ribose
-
-
?
ATP + 2-deoxy-D-ribose
ADP + 2-deoxy-D-ribose 5-phosphate
show the reaction diagram
ATP + D-arabinose
?
show the reaction diagram
-
weak activity
-
-
?
ATP + D-arabinose
ADP + D-arabinose 5-phosphate
show the reaction diagram
ATP + D-fructose
ADP + D-fructose 5-phosphate
show the reaction diagram
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-
-
-
?
ATP + D-ribose
ADP + D-ribose 5-phosphate
show the reaction diagram
ATP + D-xylose
?
show the reaction diagram
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1.06% if the activity with D-ribose
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-
?
ATP + D-xylose
ADP + D-xylose 5-phosphate
show the reaction diagram
-
-
-
-
?
CTP + D-ribose
CDP + D-ribose 5-phosphate
show the reaction diagram
dATP + D-ribose
dADP + D-ribose 5-phosphate
show the reaction diagram
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108% of the activity with ATP
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-
?
dCTP + D-ribose
dCDP + D-ribose 5-phosphate
show the reaction diagram
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25% of the activity with ATP
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-
?
dGTP + D-ribose
dGDP + D-ribose 5-phosphate
show the reaction diagram
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50% of the activity with ATP
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-
?
GTP + D-ribose
GDP + D-ribose 5-phosphate
show the reaction diagram
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32% of the activity with ATP
-
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?
ITP + D-ribose
IDP + D-ribose 5-phosphate
show the reaction diagram
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37% of the activity with ATP
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?
additional information
?
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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 + 2-deoxy-D-ribose
ADP + 2-deoxy-D-ribose 5-phosphate
show the reaction diagram
ATP + D-ribose
ADP + D-ribose 5-phosphate
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Cd2+
-
can replace Mg2+ in activation, optimal concentration: 5 mM, 68% of the activity with Mg2+
Cu2+
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can replace Mg2+ in activation, optimal concentration: 10 mM, 20% of the activity with Mg2+
Ni2+
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can replace Mg2+, optimal concentration: 25-30 mM, 31% of the activity with Mg2+
Zn2+
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can replace Mg2+ in activation, optimal concentration: 1 mM, 27% of the activity with Mg2+
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-carboxyethylphosphonic acid
clodronate
D-arabinose
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D-erythrose
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D-fructose
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D-glucose
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D-ribose
D-ribose 5-phosphate
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inhibits the phosphorylation of D-ribose
D-ribulose
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D-threose
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D-xylulose
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etidronate
Mn2+
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50 mM inhibit
N-(phosphonomethyl)-glycine
N-(phosphonomethyl)iminodiacetic acid
p-chloromercuribenzoate
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Phosphonoacetic acid
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
MtbTopA
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when increasing amounts of Mycobacterium smegmatis topoisomerase I are mixed together with ribokinase, the amount of phosphorylated D-ribose products steadily increases, indicating that Mycobacterium smegmatis topoisomerase I stimulates the kinase activity of ribokinase
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NH4+
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activates
phosphate
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increases catalytic activity. KM-for ribose and ATP decreases in a concentration-dependent manner; marked dependency upon the presence of inorganic phosphate
topoisomerase I
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when increasing amounts of MsTopA are mixed together with ribokinase, the amount of phosphorylated D-ribose products steadily increases, indicating that topoisomerase I stimulates the kinase activity of Ms4585
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.035 - 1.8
2-deoxy-D-ribose
0.04 - 4.66
ATP
0.022 - 2
D-ribose
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
10.2 - 47.81
ATP
10.8
D-ribose
Leishmania major
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4.42 - 21.87
ATP
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.2 - 18.91
ATP
0.4
D-ribose 5-phosphate
additional information
additional information
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
23.2
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77
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with D-ribose as substrate
89
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with 2-deoxy-D-ribose as substrate
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.7 - 7.3
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2-deoxy-D-ribose
7.1 - 7.8
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8
Q5HJA8
assay at
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5 - 9
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pH 5.5: about 45% of activity maximum, pH 9.0: about 55% of activity maximum
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Staphylococcus aureus (strain COL)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30800
predicted from the 307 amino acid sequence
33230
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electrospray ionization mass spectrometry
62000
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gel filtration
67800
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high-speed sedimentation equilibrium method
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
20C or 16C, hanging drop method, 7 mg/ml protein mixed with an equal volume of mother liquor
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4C, hanging drop vapour diffusion, Cs-bound ternary complex structure: P212121
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ribokinase in complex with ribose and dinucleotide: there is one 33000 Da monomer of ribokinase in the asymmetric unit but the protein forms a dimer around a crystallographic twofold axis
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several different types of crystals, apo ribokinase: space group P1 or P3x21, ATP ribokinase: tetragonal, ribose/AMP-PNP: P6x22
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crystals are obtained using the sitting-drop method. Diffraction data are collected to a resolution of 3.1 A
by using the hanging-drop vapour-diffusion method, large crystals appear at 21.85C in conditions consisting of 23% PEG 3000, 0.1 M sodium citrate pH 5.6, the crystals diffract to 2.9 A resolution and belong to space group P6122 or P6522, with unit-cell parameters a=b=91.8 A, c=160.7 A
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crystal structure of Sa239 in the absence of monovalent ions. The structure of Sa239 demonstrates that the C-terminal tail protrudes from the remaining part and interacts with the neighboring molecule, resulting in an dimerization form
Q5HJA8
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
60
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5 min, complete inactivation
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-10C gamma gel supernatants lose 64% activity in 3 months
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-12C fraction IV retains 65% activity after two months
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-70C, in buffer/glycerol (1/1), the recombinant enzyme retains more than 50% of its activity after 1 year
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
by affinity chromatography on a nickel-chelating column and gel filtration
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using affinity chromatography
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
deletion mutant is expressed in Escherichia coli
expressed in Escherichia coli
expressed in the Escherichia coli ER2566 cells harboring the constructed expression plasmid encompassing the rbsK gene
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expression in Escherichia coli
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overexpressed in Escherichia coli as a His-tagged fusion protein
overexpression in Escherichia coli
the SUMO-Sa239 fusion protein is expressed in Escherichia coli BL21 (DE3) cells
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
the gene is a part of the uriR operon, gene expression is 36.6fold stimulated by D-ribose and 9.8fold stimulated by uridine when it is containing (30 mM) in the medium, deletion of the LacI/GalR-type regulator in the mutant strain KB1546 leads to enhanced expression
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A13/103/116V
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mutant shows no interaction with topoisomerase I. Mutant only partially retains its ability to inhibit the activity of topoisomerase I even at high protein concentrations. Topoisomerase I does not significantly stimulate the activity of the mutant protein
S11N/A14V
M10N
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70 fold higher KM for deoxyribose but only 2 fold increased KM for ribose
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