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Information on EC 2.7.1.100 - S-methyl-5-thioribose kinase and Organism(s) Bacillus subtilis and UniProt Accession O31663

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IUBMB Comments
CTP also acts, but more slowly.
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This record set is specific for:
Bacillus subtilis
UNIPROT: O31663
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The taxonomic range for the selected organisms is: Bacillus subtilis
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
Synonyms
mtr kinase, 5-methylthioribose kinase, methylthioribose kinase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5-methylthioribose kinase
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5-methylthioribose kinase
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ATP:S-methylthioribose kinase
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kinase, 5-methylthioribose (phosphorylating)
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methylthioribose kinase
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phospho group transfer
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-
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PATHWAY SOURCE
PATHWAYS
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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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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-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
additional information
?
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the enzyme has significant ribose kinase activity, it has a hydrophobic pocket that specifically recognizes the methylthio group of the substrate. MTK shows a 9fold higher Vmax for ribose kinase activity than for S-methyl-5-thio-D-ribose kinase activity, but also has a several fold higher Km for ribose
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
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
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
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.06
5-methylthioribose
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37°C, approx. value
4.8
D-ribose
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pH 8.0, 25°C
0.06
S-methyl-5-thio-D-ribose
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pH 8.0, 25°C
additional information
additional information
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the Km for ribose is 80times higher than for S-methyl-5-thio-D-ribose
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
1.5
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purified recombinant non-tagged enzyme
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 8.5
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ribose kinase activity
8
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assay at
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
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assay at
25 - 35
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ribose kinase activity
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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Uniprot
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
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the enzyme catalyze the first reaction of a ribose metabolic pathway, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression as His-tagged and non-tagged enzyme in Escherichia coli strain BL21(DE3)
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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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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
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Sekowska, A.; Mulard, L.; Krogh, S.; Tse, J.K.; Danchin, A.
MtnK, methylthioribose kinase, is a starvation-induced protein in Bacillus subtilis
BMC Microbiol.
1
15
2001
Bacillus subtilis
Manually annotated by BRENDA team
Ku, S.Y.; Yip, P.; Cornell, K.A.; Riscoe, M.K.; Howell, P.L.
Crystallization and preliminary X-ray analysis of 5'-methylthioribose kinase from Bacillus subtilis and Arabidopsis thaliana
Acta Crystallogr. Sect. D
60
116-119
2004
Arabidopsis thaliana, Bacillus subtilis
Manually annotated by BRENDA team
Ku, S.Y.; Smith, G.D.; Howell, P.L.
ADP-2Ho as a phasing tool for nucleotide-containing proteins
Acta Crystallogr. Sect. D
63
493-499
2007
Bacillus subtilis (O31663), Bacillus subtilis
Manually annotated by BRENDA team
Ku, S.Y.; Yip, P.; Cornell, K.A.; Behr, J.B.; Guillerm, G.; Howell, P.L.
Structures of 5-methylthioribose kinase reveal substrate specificity and unusual mode of nucleotide binding
J. Biol. Chem.
282
22195-22206
2007
Bacillus subtilis
Manually annotated by BRENDA team
Nakano, T.; Saito, Y.; Yokota, A.; Ashida, H.
Plausible novel ribose metabolism catalyzed by enzymes of the methionine salvage pathway in Bacillus subtilis
Biosci. Biotechnol. Biochem.
77
1104-1107
2013
Bacillus subtilis
Manually annotated by BRENDA team