Information on EC 4.2.3.124 - 2-deoxy-scyllo-inosose synthase

Word Map on EC 4.2.3.124
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
Specify your search results
Select one or more organisms in this record:
Show additional data
Do not include text mining results
Include (text mining) results (more...)
Include results (AMENDA + additional results, but less precise; more...)

The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
4.2.3.124
-
RECOMMENDED NAME
GeneOntology No.
2-deoxy-scyllo-inosose synthase
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
D-glucose 6-phosphate = 2-deoxy-L-scyllo-inosose + phosphate
show the reaction diagram
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biosynthesis of antibiotics
-
-
kanamycin biosynthesis
-
-
Neomycin, kanamycin and gentamicin biosynthesis
-
-
paromamine biosynthesis I
-
-
paromamine biosynthesis II
-
-
SYSTEMATIC NAME
IUBMB Comments
D-glucose-6-phosphate phosphate-lyase (2-deoxy-scyllo-inosose-forming)
Requires Co2+ [2]. Involved in the biosynthetic pathways of several clinically important aminocyclitol antibiotics, including kanamycin, butirosin, neomycin and ribostamycin. Requires an NAD+ cofactor, which is transiently reduced during the reaction [1,4]. The enzyme from the bacterium Bacillus circulans forms a complex with the glutamine amidotransferase subunit of pyridoxal 5'-phosphate synthase (EC 4.3.3.6), which appears to stabilize the complex [6,7].
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
no activity in Streptomyces lividans
-
-
-
Manually annotated by BRENDA team
no activity in Streptomyces lividans TK24
-
-
-
Manually annotated by BRENDA team
gene allloH
-
-
Manually annotated by BRENDA team
gene btrC
-
-
Manually annotated by BRENDA team
gene btrC, a neomycin producing strain
-
-
Manually annotated by BRENDA team
gene btrC, a neomycin producing strain
-
-
Manually annotated by BRENDA team
gene btrC
-
-
Manually annotated by BRENDA team
gene kanA, encoded in the kanamycin gene cluster, no activity in strain TK24
-
-
Manually annotated by BRENDA team
gene btrC
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
metabolism
physiological function
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
2-deoxy-D-glucose 6-phosphate
2,5-dideoxy-L-scyllo-inosose + phosphate
show the reaction diagram
3-deoxy-D-glucose 6-phosphate
2,4-dideoxy-L-scyllo-inosose + phosphate
show the reaction diagram
D-glucose 6-phosphate
2-deoxy-L-scyllo-inosose + phosphate
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
D-glucose 6-phosphate
2-deoxy-L-scyllo-inosose + phosphate
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
only slightly activating, cannot substitute for Co2+
Mg2+
only slightly activating, cannot substitute for Co2+
Mn2+
only slightly activating, cannot substitute for Co2+
additional information
-
the enzyme is not affected by Mg2+, Ca2+, Mn2+, and Fe2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
carbaglucose-6-phosphate
-
a substrate analogue inhibitor, binding structure, overview. The inhibitor coordinates a cobalt ion in the active site
D-glucose 6-homophosphonate
-
competitive inhibition versus D-glucose 6-phosphate
D-glucose 6-phosphonate
-
competitive inhibition versus D-glucose 6-phosphate, hydride transfer from 6-phosphonate to NAD+
DL-carbaglucose 6-phosphate
-
a mechanism-based irreversible inhibitor, synthesis, overview. The alpha,beta-unsaturated intermediate traps a specific nucleophilic group in the active site through the Michael-type 1,4-addition. The covalently modified amino acid residue is Lys141
EDTA
-
complete inhibition
glucose-6-phosphonate
-
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.017 - 20
D-glucose 6-phosphate
additional information
additional information
-
steady state and pre-steady state kinetic analysis, overview
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.007 - 1
D-glucose 6-phosphate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00035 - 4.76
D-glucose 6-phosphate
105
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.224
DL-carbaglucose 6-phosphate
-
pH 7.7, 46°C
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.8
D-glucose 6-homophosphonate
Bacillus circulans
-
pH 7.7, 46°C
1.3
D-glucose 6-phosphonate
Bacillus circulans
-
pH 7.7, 46°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
1.1
-
purified recombinant BtrC, pH 7.7, 46°C
18.1
purified enzyme, pH 7.7, 46°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20000
1 * 40000, catalytic BtrC, + 1 * 20000, noncatalytic BtrC2, SDS-PAGE
40000
1 * 40000, catalytic BtrC, + 1 * 20000, noncatalytic BtrC2, SDS-PAGE
40608
-
x * 40608, mass spectrometry, x * 40768, DL-carbaglucose 6-phosphate-enzyme complex, mass spectrometry
40746
-
1 * 42000, BtrC, + 1 * 23000, BtrC2, recombinant enzyme, SDS-PAGE, 1 * 40746, BtrC, sequence calculation
40768
-
x * 40608, mass spectrometry, x * 40768, DL-carbaglucose 6-phosphate-enzyme complex, mass spectrometry
45000
-
x * 45000, SDS-PAGE
54000
gel filtration
65000
native PAGE
77000
-
gel filtration, recombinant enzyme
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
heterodimer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified free enzyme and enzyme in complex with substrate analogue inhibitor carbaglucose 6-phosphate, and with NAD+, and Co2+, hanging drop vapour diffusion method, mixing of 0.002 ml pf 4.2 mg/ml protein in 5 mM Tris-HCl, pH 7.7, and 0.2 mM CoCl2, with 0.002 ml of reservoir solution containing 40% w/v PEG 4000, 200 mM Li2SO4, and 100 mM Tris-HCl, pH 8.6, equilibration against 1 ml of reservoir solution, addition of 1 mM Co2+ and 1 mM inhibitor, 4°C, X-ray diffraction structure determination and analysis at 2.15-2.3 A resoltuion, heavy atom derivatization
-
purified recombinant enzyme, hanging drop vapour diffusion method, mixing of 0.002 ml pf 4.2 mg/ml protein in 5 mM Tris-HCl, pH 7.7, and 0.2 mM CoCl2, with 0.002 ml of reservoir solution containing 40% w/v PEG 4000, 200 mM Li2SO4, and 100 mM Tris-HCl, pH 8.6, equilibration against 1 ml of reservoir solution, 4°C, X-ray diffraction structure determination and analysis at 2.3 A resolution
-
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
-
purified enzyme, pH 7.5-8.5, rapid loss of activity above
80
-
crude enzyme, 5 min, inactivation
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-75°C, purified enzyme, in Tris-HCl, pH 7.7, and 0.14 M NaCl, completely stable for 6 months
4°C- -75°C, purified recombinant enzyme, in 50 mM Tris-HCl buffer with 0.2 mM Co2+, loss of 60% activity within 10 days
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
native enzyme 148fold by ammonium sulfate fractionation, anion exchange and affinity chromatography, and gel filtration, followed by another different step of anion exchange chromatography
native enzyme by ammonium sulfate fractionation, dialysis and two different steps of anion exchange chromatography
-
recombinant AlloH from Escherichia coli by anion exchange chromatography and gel filtration
-
recombinant BtrC 6.0fold from Escherichia coli strain BL21(DE3)
-
recombinant BtrC from Escherichia coli by gel filtration and hydrophobic interaction chromatography
-
recombinant BtrC2 from Escherichia coli strain JM109 by ammonium sulfate fractionation, anion exchange chromatography, ultrafiltration, and gel filtration
recombinant enzyme by gel filtration, ultracentrifugation, and hydrophobic interaction chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
complementation of a btrC2 disruption mutant by expression of wild-type btrC2 from plasmid pHB201 in Bacillus circulans
gene alloH, DNA and amino acid sequence determination and analysis, comparisons of the gene cluster with similar ones, expression in Escherichia coli
-
gene btrC, DNA and amino acid sequence determination and analysis, cloning in Escherichia coli strain JM 105, expression in Escherichia coli strain BL21(DE3)
-
gene btrC, DNA and amino acid sequence determination and analysis, cloning in Escherichia coli strain JM 105, functional expression in Escherichia coli strain BL21(DE3)
-
gene btrC, DNA and amino acid sequence determination and analysis, sequence comparisons, overexpression in Escherichia coli strain BL21(DE3)
gene btrC, expression in Escherichia coli
-
gene btrC, recombinant expression
-
gene DOIS, expression in Escherichia coli strain GI724 from plasmid pGA-btrC
-
gene kanA, expression in Escherichia coli strains XL1-Blue MRF and BL21 (DE3), in the latter as His6-tagged protein, using plasmid pIBR25, formation of insoluble KanA, expression in Streptomyces lividans strain TK24 using pIBR25 with a MCS is successful
-
genes btrC and btrC2, co-overexpression in Escherichia coli strain JM109
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
BtrC expression is highly reduced by supplementation with 0.01 mg/ml pyridoxal
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E243Q
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
K141Q
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
industry