Information on EC 2.7.1.17 - xylulokinase

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

EC NUMBER
COMMENTARY hide
2.7.1.17
-
RECOMMENDED NAME
GeneOntology No.
xylulokinase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + D-xylulose = ADP + D-xylulose 5-phosphate
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phospho group transfer
-
-
-
-
Phosphorylation
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
D-arabitol degradation
-
-
degradation of sugar alcohols
-
-
Metabolic pathways
-
-
Pentose and glucuronate interconversions
-
-
xylitol degradation
-
-
xylose degradation I
-
-
SYSTEMATIC NAME
IUBMB Comments
ATP:D-xylulose 5-phosphotransferase
-
CAS REGISTRY NUMBER
COMMENTARY hide
9030-58-4
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
expression in Escherichia coli
-
-
Manually annotated by BRENDA team
calf
-
-
Manually annotated by BRENDA team
strain Xu316
UniProt
Manually annotated by BRENDA team
strain Xu316
UniProt
Manually annotated by BRENDA team
Escherichia coli DH5-alpha
strain DH5alpha
-
-
Manually annotated by BRENDA team
DSM 12041
-
-
Manually annotated by BRENDA team
var. aerogenes 1033, formerly Aerobacter aerogenes 1033, mutant strain KAY2026
-
-
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
strain 124-2
-
-
Manually annotated by BRENDA team
strain 124-2
-
-
Manually annotated by BRENDA team
Ogataea angusta XRm/XDH/XK
strain XRm/XDH/XK, overexpression of XK, thermotolerant
-
-
Manually annotated by BRENDA team
Ogataea angusta XRn/XDH/XK
strain XRn/XDH/XK, overexpression of XK, thermotolerant
-
-
Manually annotated by BRENDA team
strain CBS 8066
Uniprot
Manually annotated by BRENDA team
Saccharomyces cerevisiae D452-2 D-XR/ARSdR
strain D452-2 D-XR/ARSdR
-
-
Manually annotated by BRENDA team
Saccharomyces cerevisiae D452-2 D-XR/ARSdR/XK
strain D452-2 D-XR/ARSdR/XK
-
-
Manually annotated by BRENDA team
Saccharomyces cerevisiae D452-2 D-XR/XDH
strain D452-2 D-XR/XDH
-
-
Manually annotated by BRENDA team
Saccharomyces cerevisiae D452-2 D-XR/XDH/XK
strain D452-2 D-XR/XDH/XK
-
-
Manually annotated by BRENDA team
strain L2612
-
-
Manually annotated by BRENDA team
W303-1B
-
-
Manually annotated by BRENDA team
strain FPL-YS30
-
-
Manually annotated by BRENDA team
over-expression onf enzyme
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
metabolism
physiological function
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engineered Saccharomyces cerevisiae overexpressing GRE3, XYL2, and XYL3 can ferment xylose as well as a mixture of glucose and xylose with higher ethanol yields and productivities than those of an isogenic strain overexpressing XYL1, XYL2, and XYL3 under oxygen-limited conditions
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + 1-deoxy-D-xylulose
ADP + 1-deoxy-D-xylulose 5-phosphate
show the reaction diagram
ATP + D(+)-arabitol
ADP + D(+)-arabitol 5-phosphate
show the reaction diagram
ATP + D(-)-arabinose
ADP + D(-)arabinose 5-phosphate
show the reaction diagram
ATP + D-arabitol
ADP + D-arabitol 5-phosphate
show the reaction diagram
-
-
-
?
ATP + D-fructose
ADP + D-fructose 5-phosphate
show the reaction diagram
ATP + D-glucose
ADP + D-glucose 6-phosphate
show the reaction diagram
ATP + D-ribose
ADP + D-ribose 5-phosphate
show the reaction diagram
ATP + D-ribulose
ADP + D-ribulose 5-phosphate
show the reaction diagram
ATP + D-xylitol
ADP + ?
show the reaction diagram
121% relative activity compared to D-glucose
-
-
?
ATP + D-xylitol
ADP + D-xylitol-1-phosphate
show the reaction diagram
-
analyzed with 31P NMR spectrum
-
-
?
ATP + D-xylitol
ADP + D-xylitol-5-phosphate
show the reaction diagram
-
analyzed with 31P NMR spectrum
-
-
?
ATP + D-xylose
ADP + D-xylose 5-phosphate
show the reaction diagram
85% relative activity compared to D-glucose
-
-
?
ATP + D-xylulose
?
show the reaction diagram
ATP + D-xylulose
ADP + D-xylulose 5-phosphate
show the reaction diagram
ATP + L(-)-arabitol
ADP + L(-)-arabitol 5-phosphate
show the reaction diagram
93% relative activity compared to D-glucose
-
-
?
ATP + L-arabinose
ADP + L-arabinose 5-phosphate
show the reaction diagram
96% relative activity compared to D-glucose
-
-
?
ATP + L-erythrulose
ADP + ?
show the reaction diagram
-
phosphorylation at 30% the rate of D-xylulose
-
-
?
ATP + ribitol
ADP + ?
show the reaction diagram
41% relative activity compared to D-glucose
-
-
?
ATP + xylitol
ADP + ?
show the reaction diagram
CTP + 1-deoxy-D-xylulose
CDP + 1-deoxy-D-xylulose 5-phosphate
show the reaction diagram
D-xylulose + ATP
D-xylulose 5-phosphate + ADP
show the reaction diagram
-
-
-
-
?
GTP + 1-deoxy-D-xylulose
GDP + 1-deoxy-D-xylulose 5-phosphate
show the reaction diagram
-
38% of the activity with ATP
-
?
GTP + D-xylulose
GDP + D-xylulose 5-phosphate
show the reaction diagram
ITP + 1-deoxy-D-xylulose
IDP + 1-deoxy-D-xylulose 5-phosphate
show the reaction diagram
-
26% of the activity with ATP
-
?
ITP + D-xylulose
IDP + D-xylulose 5-phosphate
show the reaction diagram
-
phosphorylation at 25% the rate of ATP
-
-
?
L-ribulose + ATP
L-ribulose 5-phosphate + ADP
show the reaction diagram
-
-
-
-
?
UTP + 1-deoxy-D-xylulose
UDP + 1-deoxy-D-xylulose 5-phosphate
show the reaction diagram
UTP + D-xylulose
UDP + D-xylulose 5-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
ATP + 1-deoxy-D-xylulose
ADP + 1-deoxy-D-xylulose 5-phosphate
show the reaction diagram
ATP + D-xylulose
?
show the reaction diagram
ATP + D-xylulose
ADP + D-xylulose 5-phosphate
show the reaction diagram
D-xylulose + ATP
D-xylulose 5-phosphate + ADP
show the reaction diagram
-
-
-
-
?
L-ribulose + ATP
L-ribulose 5-phosphate + ADP
show the reaction diagram
-
-
-
-
?
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ni2+
-
activation, half as effective as Mg2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5-deoxy-5-fluoro-D-xylulose
-
5-fluoro-xylulose
0.18 mM, strong inhibition of the ATPase activity of xylulokinase
ADP
-
product inhibition
ATP
-
additional Mg2+ reverses
Mg2+
-
above 0.08 mM
PCMB
-
cysteine reverses
additional information
-
no inhibition by F- or iodoacetate
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
DTT
-
enzyme is inactive in absence either EDTA or a thiol such as reduced monosodium glutathione or dithiothreitol
Monosodium glutathione
-
enzyme is inactive in absence either EDTA or a thiol such as reduced monosodium glutathione or dithiothreitol
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.28
ADP
1.55 - 8.2
ATP
141
D-arabitol
wild type enzyme
14
D-ribulose
wild type enzyme
0.024 - 0.8
D-xylulose
1.3
D-xylulose 5-phosphate
-
pH 6.5, 30C
0.16
MgATP2-
-
pH 8.0, 25C
127
xylitol
wild type enzyme
0.09
xylulose
-
pH 8.0, 25C
additional information
additional information
-
radiometric system for measurement of enzyme activity in crude cell extracts
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0038 - 0.5
ATP
105
D-arabitol
Escherichia coli
P09099
wild type enzyme
235
D-ribulose
Escherichia coli
P09099
wild type enzyme
0.64 - 6600
D-xylulose
237
xylitol
Escherichia coli
P09099
wild type enzyme
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1500
D-xylulose
Homo sapiens
O75191
in 50 mM NH4HCO3, pH 8.0, 10% (v/v) D2O, 10 mM MgCl2 at 25C
715
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.025
5-deoxy-5-fluoro-D-xylulose
in 50 mM NH4HCO3, pH 8.0, 10% (v/v) D2O, 10 mM MgCl2 at 25C
0.026 - 0.15
5-fluoro-xylulose
0.71 - 1.9
AMPPNP
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.134
-
Pseudomonas putida S12 strain xylAB containing xylose isomerase and xylulokinase gene from Escherichia coli
1.6
-
reaction with 1-deoxy-D-xylulose
4.1
-
-
23.5
using D-xylulose as substrate, 50 mM Tris-HCl (pH 7.5), at 25C
46
using D-fructose as substrate, 50 mM Tris-HCl (pH 7.5), at 25C
51
-
reaction with D-xylulose
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 10
-
about half-maximal activity at pH 6 and 10
6.7 - 9
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pH 6.7: about 50% of maximal activity, pH 9.0: about 75% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10 - 40
-
steady increase up to 30C, rapid loss above, with 60% of maximal activity at 40C
30 - 77
-
30C: about 50% of maximal activity, 77C: about 65% of maximal activity
37 - 38
-
-
45 - 48
-
-
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
Pseudomonas strain S12 containing xylose isomerase gene and xylulokinase gene from Escherichia coli strain DH5 alpha
Manually annotated by BRENDA team
-
xylulokinase activity is absent during glucose metabolism but is detectable during simultaneous utilization of xylulose and glucose
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757)
Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757)
Cryptosporidium parvum (strain Iowa II)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIB 8255 / S1)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
61830
-
calculated from amino acid sequence
68000
-
SDS-PAGE
68890
calculated from amino acid sequence
110000 - 115000
-
gel filtration
110000
120000 - 130000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop vapour diffusion method using 1.5 M ammonium sulfate, 50 mM sodium citrate, pH 6, 1% (w/v) t-butanol and 25% (v/v) ethylene glycol, at 25C
hanging drop vapor diffusion method, using 200 mM MES-KOH pH 6.0, 16% (w/v) PEG 6000
-
sitting drop vapor diffusion method, using 200 mM MES-KOH, pH 6.0, 16% (w/v) polyethylene glycol 6000, 0.3 mM NaN3
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.4
-
5 min, 26% loss of activity at 53C, inactivation at 60C
645053
5.7
-
5 min, 30% loss of activity at 53C
645053
6.2
-
5 min, 50% loss of activity at 53C
645053
7
-
5 min, 60% loss of activity at 53C
645053
8
-
5 min, 66% loss of activity at 53C
645053
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4
-
inactivation, only partially reversible by incubation at 37C
10 - 50
-
more than 50% of the optimum activity between 10C and 50C
53
-
5 min, 66%, 60%, 50%, 30% or 26% loss of activity at pH 8, pH 7, pH 6.2, pH 5.7 and pH 5.4, respectively
60
-
5 min, inactivation at pH 5.4
65
-
30 min, Tris buffer, stable up to
70
-
30 min, 50% loss of activity
75
-
8 mM xylulose, 55% loss of activity after 30 min, 15% loss of activity after 5 min
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
D-xylulose, ATP, glycerol and EDTA stabilize
-
EDTA and MgCl2 partially stabilize
-
repeated freeze-thawing inactivates, sulfhydryl compounds do not stabilize
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-12C, ammonium sulfate precipitate, over 1 month
-
-20C, 1 month stable and 20% of original activity retained after 8 months
-
-20C, about 30% of original activity retained after 4 years
-
-80C, 50 mM Tris/HCl, pH 7.8, 12.5% (w/v) glycerol, 1 month
-
0C, several months
-
4C, 1 mg protein/ml in 0.1 M potassium phosphate buffer, pH 7, 2 mM MgCl2, 0.1 mM EDTA, 0.1 mM PMSF, 10 mM 2-mercaptoethanol, 90% loss of activity within 18 h
-
4C, inactivation within 24 h
-
enzyme preparations are generally very unstable and lose their activity within a few days
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
apo-enzyme and in complex with D-xylulose, ATP plus D-xylulose or 5-deoxy-5-fluoro-D-xylulose, nickel affinity column chromatography and Superdex 200 gel filtration
harvested cells resuspended in 50 mM Tris/HCl pH 7.8, solution after ultrasonically disruption centrifuged at 10000 *g for 30 min at 4C, supernatant passed through immobilized metal affinity chromatography (5 ml) using the His-tag introduced into the C-terminal region of XK, purified enzyme dialyzed against 50 mM Tris/Hcl (pH 7.8) containing 12.5% (w/v) glycerol
-
Ni-NTA column chromatography and Sephacryl S200 gel filtration
nickel affinity column chromatography and Superdex 200 gel filtration
-
partial
partial purification using Sepharose-Q column chromatography
-
recombinant enzyme
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cloning and functional expression of enzymes from Escherichia coli in Pseudomonas putida
-
expressed in Escherichia coli
-
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli K12 strain NC260 harbouring multi-copy lambdaprbt-101 dal-201 prophage
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expressed in Escherichia coli strain PC07 with deleted xylB-gene and introduced plasmid with Escherichia coli xylB gene
-
expressed in Escherichia coli strain PC07, xyl3 gene from Pichia stipitis
-
expressed in Escherichia coli strain XL1-Blue (Stratagene)
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expressed in Hansenula polymorpha strain CBS4732 double mutant with deleted genes of both XR (xylose reductase) and XDH (NAD-dependent xylitol dehydrogenase), expression driven by the Hansenula polymorpha glyceraldehyde-3-phosphate dehydrogenase promoter
-
expressed in Hansenula polymorpha strain CBS4732s leu2-2
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expressed in Saccharomyces cerevisiae strain D452-2, DNA from Saccharomyces cerevisiae strain S288C, strain D-XR/ARSdR with naturally occuring XK-activity; expressed in Saccharomyces cerevisiae strain D452-2, DNA from Saccharomyces cerevisiae strain S288C, strain D-XR/ARSdR/XK with upegulated XK-activity, entire coding sequence of XK with PGK promoter and terminator inserted into pAUR101 shuttle vector (Takara Bio, Kyoto) integrating in Saccharomyces cerevisiae strain D452-2; expressed in Saccharomyces cerevisiae strain D452-2, DNA from Saccharomyces cerevisiae strain S288C, strain D-XR/XDH with naturally occuring enzyme-activity; expressed in Saccharomyces cerevisiae strain D452-2, DNA from Saccharomyces cerevisiae strain S288C, strain D-XR/XDH/XK with upegulated XK-activity, entire coding sequence of XK with PGK promoter and terminator inserted into pAUR101 shuttle vector integrating in Saccharomyces cerevisiae strain D452-2
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expressed in Saccharomyces cerevisiae strain DX23
-
expressed in Saccharomyces cerevisiae strain W303-1B and Escherichia coli strain TOP10
expressed in Saccharomyces cerevisiae under the control of the glyceraldehyde 3-phosphate dehydrogenase promoter and terminator
-
expressed in Zymobacter palmae
-
expression in Escherichia coli. Expression of XYL3 using its Pichia stipitis promoter increase Saccharomyces cerevisiae D-xylulose consumption 3fold and enables the transformants to produce ethanol from a mixture of xylulose and xylose, whereas the parental strain only accumulates xylitol. In vitro, D-xylulokinase activity in recombinant Saccharomyces cerevisiae is sixfold higher with a multicopy than with a single-copy XYL3 plasmid, but ethanol production decreases with increased copy number
-
overexpression in Saccharomyces cerevisiae
-
overexpression of the gene on Saccharomyces cerevisiae H158 and CEN-PK also expressing xylose reductase and xylitol dehydrogenase. Effect on fermentation of xylose and lignocellulosic hydrolysate
overexpression of xylulokinase in Saccharomyces cerevisiae is detrimental to cell growth on xylulose but not on glucose
recombinant XYL3 gene driven by the HpGAP promotor transformed into the recipient strain Hansenula polymorpha; recombinant XYL3 gene driven by the HpGAP promotor transformed into the recipient strain H. polymorpha
-
use of Pichia stipitis strain FPL-YS30 without D-xylulokinase-activity cause in the deletion of gene xyl3
-
xylB gene expressed in Escherichia coli K12
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D233A
loss of activity
D6A
19fold decreased ATPase activity compared to the wild type enzyme
DELTAxyl3
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biotechnology
-
putative use of lignocellulosic biomass as feedstock for the chemical industry
synthesis
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