Information on EC 2.7.1.100 - S-methyl-5-thioribose kinase

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

EC NUMBER
COMMENTARY hide
2.7.1.100
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RECOMMENDED NAME
GeneOntology No.
S-methyl-5-thioribose kinase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + S-methyl-5-thio-D-ribose = ADP + S-methyl-5-thio-alpha-D-ribose 1-phosphate
show the reaction diagram
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-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phospho group transfer
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-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Cysteine and methionine metabolism
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Metabolic pathways
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S-methyl-5'-thioadenosine degradation I
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methionine metabolism
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SYSTEMATIC NAME
IUBMB Comments
ATP:S-methyl-5-thio-D-ribose 1-phosphotransferase
CTP also acts, but more slowly.
CAS REGISTRY NUMBER
COMMENTARY hide
68247-56-3
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
red
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Manually annotated by BRENDA team
yellow lupin
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Manually annotated by BRENDA team
appletree, Golden delicious
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
d'Anjou
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-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
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although most bacteria, yeasts, and animals have the complete methionine salvage pathway, MSP enzymes, these organisms have 5-methylthioadenosine phosphorylase, MtnP, instead of MtnK
metabolism
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
alphaATP + 5-methylthioribose
alphaADP + 5-methylthioribose 1-phosphate
show the reaction diagram
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-
-
?
ATP + 5-butylthioribose
ADP + 5-butylthioribose 1-phosphate
show the reaction diagram
-
-
-
?
ATP + 5-ethylthioribose
ADP + 5-ethylthioribose 1-phosphate
show the reaction diagram
-
-
-
?
ATP + 5-isobutylthioribose
ADP + 5-isobutylthioribose 1-phosphate
show the reaction diagram
ATP + 5-isopropylthioribose
ADP + 5-isopropylthioribose 1-phosphate
show the reaction diagram
-
-
-
?
ATP + 5-methyl-5-thio-D-ribose
ADP + 5-methyl-5-thio-D-ribose 1-phosphate
show the reaction diagram
ATP + 5-methylthioribose
ADP + 5-methylthioribose 1-phosphate
show the reaction diagram
ATP + 5-propylthioribose
ADP + 5-propylthioribose 1-phosphate
show the reaction diagram
-
-
-
?
ATP + D-ribose
ADP + D-ribose 1-phosphate
show the reaction diagram
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-
-
-
?
ATP + S-methyl-5-thio-D-ribose
ADP + S-methyl-5-thio-alpha-D-ribose 1-phosphate
show the reaction diagram
ATP + S-methyl-5-thio-D-ribose
ADP + S-methyl-5-thio-D-ribose 1-phosphate
show the reaction diagram
CTP + 5-methylthioribose
CDP + 5-methylthioribose 1-phosphate
show the reaction diagram
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20% of activity with ATP
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?
dATP + 5-methylthioribose
dADP + 5-methylthioribose 1-phosphate
show the reaction diagram
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120% of 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 + 5-methyl-5-thio-D-ribose
ADP + 5-methyl-5-thio-D-ribose 1-phosphate
show the reaction diagram
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-
-
-
?
ATP + 5-methylthioribose
ADP + 5-methylthioribose 1-phosphate
show the reaction diagram
ATP + S-methyl-5-thio-D-ribose
ADP + S-methyl-5-thio-alpha-D-ribose 1-phosphate
show the reaction diagram
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physiological substrate
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-
?
ATP + S-methyl-5-thio-D-ribose
ADP + S-methyl-5-thio-D-ribose 1-phosphate
show the reaction diagram
additional information
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ho3+
trivalent holmium ions can isomorphously replace Mg2+ form an ADP-2Ho complex in the nucleotide-binding domain of Bacillus subtilis 5-methylthioribose kinase The structure of ADP-2Ho reveals that the two Ho ions are approximately 4 A apart and are likely to share their ligands: the phosphoryl O atoms of ADP and a water molecule
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-oxo-4-methylthiobutyrate
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1 mM, 10% inhibition
5-Ethylthioribose
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weak inhibition
5-Isobutylthioribose
5-Isopropylthioribose
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weak inhibition
adenine
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1 mM, 25% inhibition
CTP
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in the presence of ATP
p-chloromercuribenzoate
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S-adenosylhomocysteine
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1 mM, 36% inhibition
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-mercaptoethanol
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20 mM, 70% of activity with dithiothreitol
dithiothreitol
glutathione
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20 mM, 44% of activity with dithiothreitol
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0043 - 0.06
5-methylthioribose
0.0083 - 0.074
ATP
4.8
D-ribose
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pH 8.0, 25C
0.0168 - 0.06
S-methyl-5-thio-D-ribose
additional information
additional information
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0014
5-Isobutylthioribose
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.0007
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activity in fruit at breaker stage of ripening
0.1425
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1
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purified recombinant His-tagged enzyme
1.5
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purified recombinant non-tagged enzyme
additional information
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mapping of secondary structural elements by in silico analysis, effect of pH on kinase activity, structure compared to enzyme structure of Bacilus subtilis, same protein kinase fold observed in other evolutionary related protein kinase-like phosphotransferases
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 8.5
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ribose kinase activity
10 - 10.5
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 10.5
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approx. 25% of maximal activity at pH 7.0
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25 - 35
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ribose kinase activity
35
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assay at
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
strong upregulation of enzyme expression during sulfur starvation
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
46000
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1 * 46000, SDS-PAGE
48600
x * 48600, SDS-PAGE, x * 50000, recombinant enzyme, SDS-PAGE
70000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 48600, SDS-PAGE, x * 50000, recombinant enzyme, SDS-PAGE
monomer
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1 * 46000, SDS-PAGE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified recombinant His-tagged enzyme, hanging drop vapour diffusion method, 0.002 ml of protein solution containing 10 mg/ml protein in 20 mM imidazole, pH 7.6, 2 mM DTT, 1 mM 5-methyl-5-thio-D-ribose and 1 mM ATP-gamma-S, is mixed an equal volume of reservoir solution containing 10% w/v PEG 8000, 0.1 M sodium cacodylate, pH 6.5, and 0.2 M magnesium acetate, equilibration against 0.5 ml reservoir solution, room temperature, 3 days, cryoprotection by soaking in reservoir solution plus 25% v/v ethylene glycol, X-ray diffraction structure determination and analysis at 1.9 A resolution, identification of heavy-atom derivatives
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structure determination, 1.9 A resolution, diffraction data and crystallographic refinement statistics, similarity to enzyme structure of Bacillus subtilis, conformation of Gly-rich loop more extended in Arabidopsis thaliana than in bacterial enzyme homologues, different conformations of G-loops and W-loops in Arabidopsis thaliana and Bacillus subtilis enzymes despite of high sequence similarities, significant ATPase activity in the absence of 5-methyl-5-thio-D-ribose suggested, features of the substrate binding site offer opportunities for a simple organic salt of a 5-methyl-5-thio-D-ribose analog to specifically inhibit kinase activity
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ADP-2Ho and ADP-2Mg complexes
purified recombinant non-tagged enzyme, hanging drop vapour diffusion method, 0.002-0.003 ml of protein solution containing 7.5-15 mg/ml protein in 10 mM potassium phosphate, pH 7.4, 2 mM DTT, 1 mM 5-methyl-5-thio-D-ribose and 1 mM ATP-gamma-S, or 8 mM CHAPS, is mixed an equal volume of reservoir solution containing 22% w/v PEG 2000 monomethylether, 0.1 M Tris-HCl, pH 7.5, and 0.3 M sodium acetate, equilibration against 0.5 ml reservoir solution, room temperature, 3 days, cryoprotection by soaking in reservoir solution plus 25% v/v ethylene glycol, X-ray diffraction structure determination and analysis at 3.0 A resolution without detergent, and at 2.2 A resolution in presence of CHAPS, no crystallization of His-tagged enzyme possible, identification of heavy-atom derivatives
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, 20% glycerol, at least 5 mg/ml, stable
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate, aminohexyl-Sepharose, Sephadex g-200, hydroxyapatite Bio-Gel
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ammonium sulfate, DEAE-Sepharose, 5-(p-aminophenyl)thioribose affinity chromatography
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ammonium sulfate, partial purified
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ammonium sulfate, Sephadex G-200, DEAE-cellulose
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purified from inclusion bodies, gel filtration
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recombinant GST-fusion protein from Escherichia coli by glutathione affinity chromatography, the GST-tag is cleaved off
recombinant His-tagged and non-tagged enzymes from Escherichia coli strain BL21(DE3), the latter by anion exchange chromatography, ultracentrifucation and gel filtration
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recombinant refolded His-tagged enzyme from Escherichia coli by centrifugation, nickel affinity chromatography, ultrafiltration and gel filtration
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis
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DNA and amino acid sequence determination and analysis, overvexpression of a slightly modified enzyme in Escherichia coli strain BL21 as GST-fusion protein
expressed in Escherichia coli
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expression as His-tagged and non-tagged enzyme in Escherichia coli strain BL21(DE3)
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expression as His-tagged enzyme in Escherichia coli strain BL21(DE3) in inclusion bodies
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gene MTK1, quantitative realtime PCR enzyme expression analysis
gene mtnK, encoded in the mtnKA operon
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structure determination of apo-MTR kinase and its substrate complexes with ADP, ADP-PO4 and beta,gamma-methyleneadenosine 5'-triphosphate
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
both in Arabidopsis and in Plantago, the Yang cycle enzymes are encoded by highly vasculature-specific genes or by genes showing much stronger expression in the vasculature than in nonvascular tissue. There are high expression levels of S-adenosyl methionine decarboxylases in the vasculature of Arabidopsis and Plantago
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both in Arabidopsis and in Plantago, the Yang cycle enzymes are encoded by highly vasculature-specific genes or by genes showing much stronger expression in the vasculature than in nonvascular tissue. There are significantly higher concentrations of Met, S-adenosyl methionine, and 5-methylthioadenosine and a less pronounced enrichment of polyamines in Plantago vascular versus nonvascular tissue and high expression levels of S-adenosyl methionine decarboxylases in the vasculature of Arabidopsis and Plantago
proteomic analysis of rice root proteins in untreated and in roots infected with Herbaspirillum seropedicae SmR1, overview. The 5-methylthioribose kinase is upregulated. quantitative realtime PCR expression analysis also confirms that the methionine recycling genes are upregulated in rice roots colonized by bacteria
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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insertional mutagenesis results in inability of the plants to grow on methylthioadenosine as asupplemntal sulfur source, knockout plants show unimpaired growth under standard conditions
Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
solubilization and refolding of His-tagged enzyme from Escherichia coli inclusion bodies by 6 M guanidium hydrochloride, 0.7 M NaCl, and 20 mM imidazole, at pH 8.0, 30 min at 4C
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
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5-methylthioribose kinase is a key enzyme in methionine salvage in bacteria and the absence of a mammalian homolog suggests that it is a good target for the design of novel antibiotics
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