Information on EC 5.4.2.7 - phosphopentomutase

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

EC NUMBER
COMMENTARY hide
5.4.2.7
-
RECOMMENDED NAME
GeneOntology No.
phosphopentomutase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
alpha-D-ribose 1-phosphate = D-ribose 5-phosphate
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
group transfer
-
-
intramolecular, phosphate group
-
isomerization
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
2'-deoxy-alpha-D-ribose 1-phosphate degradation
-
-
Pentose phosphate pathway
-
-
PRPP biosynthesis II
-
-
Purine metabolism
-
-
purine ribonucleosides degradation
-
-
purine metabolism
-
-
SYSTEMATIC NAME
IUBMB Comments
alpha-D-ribose 1,5-phosphomutase
Also converts 2-deoxy-alpha-D-ribose 1-phosphate into 2-deoxy-D-ribose 5-phosphate. alpha-D-Ribose 1,5-bisphosphate, 2-deoxy-alpha-D-ribose 1,5-bisphosphate, or alpha-D-glucose 1,6-bisphosphate can act as cofactor.
CAS REGISTRY NUMBER
COMMENTARY hide
9026-77-1
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain AKU 229
UniProt
Manually annotated by BRENDA team
strain AKU 229
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
wild-type and regulatory mutants
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
-
only a deletion mutant of PGM3, not of PGM1 or PGM2, hyperaccumulates ribose-1-phosphate, and shows a strongly increased concentration of ribose 1-phosphate and completely defective recycling of ribose 1-phosphate upon glucose-induced purine nucleoside recycling via the purine salvage pathway
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
2,3-dideoxyribose 5-phosphate
2,3-dideoxyribose 1-phosphate
show the reaction diagram
2-deoxy-D-ribose 1-phosphate
2-deoxy-D-ribose 5-phosphate
show the reaction diagram
-
-
-
?
2-deoxy-D-ribose 5-phosphate
2-deoxy-D-ribose 1-phosphate
show the reaction diagram
2-deoxyribose 5-phosphate
2-deoxyribose 1-phosphate
show the reaction diagram
2-Deoxyribose 5-phosphate
?
show the reaction diagram
-
-
-
-
-
alpha-D-arabinose 5-phosphate
alpha-D-arabinose 1-phosphate
show the reaction diagram
-
-
-
-
?
alpha-D-pentose 5-phosphate
alpha-D-pentose 1-phosphate
show the reaction diagram
-
-
-
-
?
alpha-D-ribose 1-phosphate
alpha-D-ribose 5-phosphate
show the reaction diagram
alpha-D-ribose 1-phosphate
D-ribose 5-phosphate
show the reaction diagram
arabinose 5-phosphate
arabinose 1-phosphate
show the reaction diagram
-
-
-
r
D-Arabinose 5-phosphate
D-Arabinose 1-phosphate
show the reaction diagram
D-ribose 1-phosphate
D-ribose 5-phosphate
show the reaction diagram
Deoxyribose 1-phosphate
Deoxyribose 5-phosphate
show the reaction diagram
Glucose 1-phosphate
?
show the reaction diagram
-
at 2.4% of the activity relative to ribose 1-phosphate
-
-
-
Ribose 1-phosphate
?
show the reaction diagram
-
inducible enzyme. In order to enter the pentose phosphate cycle ribose 1-phosphate must be isomerized to ribose 5-phosphate
-
-
-
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
2-Deoxyribose 5-phosphate
?
show the reaction diagram
-
-
-
-
-
alpha-D-ribose 1-phosphate
alpha-D-ribose 5-phosphate
show the reaction diagram
alpha-D-ribose 1-phosphate
D-ribose 5-phosphate
show the reaction diagram
Ribose 1-phosphate
?
show the reaction diagram
-
inducible enzyme. In order to enter the pentose phosphate cycle ribose 1-phosphate must be isomerized to ribose 5-phosphate
-
-
-
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
-
activity is dependent on Mn2+, Ni2+ or Co2+. Optimal concentration: 0.05-0.06 mM
Zn2+
1 mM, 45% of the activation with Mg2+
additional information
-
not dependent on Zn2+, Ni2+, Mg2+, and Co2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
AsO43-
-
-
Ca2+
-
in presence of 0.2 mM CoCl2
Cd2+
-
in presence of 0.2 mM CoCl2
Cu2+
-
in presence of 0.2 mM CoCl2
Fe3+
-
in presence of 0.2 mM CoCl2
phosphate
-
50 mM, 95% inhibition
SO42-
-
50 mM, 85% inhibition
Zn2+
-
in presence of 0.2 mM CoCl2
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
D-Glucose 1,6-bisphosphate
D-glucose 1,6-diphosphate
-
-
Deoxyribose-1,5-diphosphate
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10fold stimulation, Km: 0.00017 mM, optimal concentration: 0.0014 mM
glucose 1,6-bisphosphate
-
required for activation. The conformational change in Lys240 alters the affinity of the enzyme for the activator
glucose 1,6-diphosphate
ribose-1,5-diphosphate
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.5
2-deoxy-D-ribose 1-phosphate
90C
0.5 - 3
alpha-D-ribose 1-phosphate
0.263
D-ribose 5-phosphate
-
in 25 mM Tris-HCl, pH 8.0, and 0.1 mM MnCl2, 0.0005 mM glucose 1,6-bisphosphate,at 23C
0.013 - 0.083
deoxyribose 1-phosphate
0.043 - 0.13
ribose 1-phosphate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
173
2-deoxy-D-ribose 1-phosphate
Thermococcus kodakarensis
Q6I7B6
90C
10.2
D-ribose 5-phosphate
Bacillus cereus
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in 25 mM Tris-HCl, pH 8.0, and 0.1 mM MnCl2, 0.0005 mM glucose 1,6-bisphosphate,at 23C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.06
-
purified recombinant His-tagged Pgm1, pH 7.5, 30C
0.29
-
purified recombinant His-tagged Pgm3, pH 7.5, 30C
0.32
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purified recombinant His-tagged Pgm2, pH 7.5, 30C
additional information
-
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5 - 8.5
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20 - 22
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assay at
65
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at pH 8.0; ribose 1-phosphate synthesis, at pH 8.0
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
70 - 100
70C: about 55% of maximal activity, 100C: about 90% of maximal activity
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.85
-
isoelectric focusing
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711)
Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
32000
-
gel filtration
32500
-
2 * 32500, SDS-PAGE
43735
-
1 * 43735, calculation from nucleotide sequence; 1 * 43735, deduced from nucleotide sequence
44000
-
x * 44000, SDS-PAGE
45000
-
equilibrium centrifugation
46000
determined by SDS-PAGE
48000
-
1 * 48000, SDS-PAGE
53000
-
gel filtration
65000
-
disc gel electrophoresis
86000
-
gel filtration
210000
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
-
2 * 32500, SDS-PAGE
monomer
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphoprotein
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
enzyme alone, co-crystallized with ribose 5-phosphate, co-crystallized with glucose 1,6-bisphosphate, and following activation with glucose 1,6-bisphosphate, hanging drop vapor diffusion method, using 100 mM Bis-Tris, pH 5.5, 50 mM MnCl2, 14% (w/v) polyethylene glycol 3350, and 75 mM NH4CH3COO
-
hanging drop vapor diffusion method, using 100 mM Bis-Tris pH 5.5, 50 mM MnCl2, 13-16% PEG 3350, and 25-100 mM NH4CH3COO; hanging drop vapor diffusion method, using 100 mM Bis-Tris pH 5.5, 50 mM MnCl2, 13-16% PEG 3350, and 25-100 mM NH4CH3COO
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purified recombinant detagged wild-type and mutant T85Q and T85E enzymes free or in complex with glucose 1,6-bisphosphate, hanging drop vapor diffusion method, for the free enzyme crystals: mixing of 10 mg/ml protein in 25mM Tris-HCl, pH 7.5, and 1 mM MnCl2, with reservoir solution containing 100 mM Bis-Tris, pH 5.5, 50 mM MnCl2, 17% PEG 3350 (wild-type) or 13% PEG 3350 (mutant T85Q), and 75 mM NH4CH3COO, for the complex crystals: mixing of 10 mg/ml protein in 5 mM glucose 1,6-bisphosphate, 25 mM Tris-HCl, pH 7.4, and 1 mM MnCl2 with a reservoir solution containing 100 mM Bis-Tris, pH 5.5, 50 mM MnCl2, 14% PEG 3350, and 50 mM NH4CH3COO, X-ray diffraction structure determination and analysis at 1.8-2.3 A resolution
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 9
-
50C, 1 h, stable
3348
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
-
half-life of the cobalt-enzyme in 1 mM EDTA: 15 min for enzyme form I, 31 min for enzyme form II
55 - 70
-
no loss of activity at 55C at pH 8.0 after 15 min, complete loss of activity after 15 min at 70C and pH 8.0
55
-
pH 8.0, 15 min, completely stable below
70
-
pH 8.0, 15 min, stable
100
half-life: 90 min
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
glucose 1,6-diphosphate protects against thermal inactivation
-
the phosphoenzyme is stable throughout purification and crystallization
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4C, Tris buffer or phosphate buffer, pH 7-8, stable for 1 month
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
HisTrap HP column chromatography and Superdex 200 gel filtration
-
multiple forms: I, II, II-1 and III-2
-
recombinant His-tagged Pgm1, Pgm2, and Pgm3 from Escherichia coli strain BL21 (DE3)
-
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, His-tag removal by thrombin cleavage, followed by gel filtration
-
recombinant PPM, Toyopearl HW-55, DEAE-Toyopearl, Butyl-Toyopearl, Sephacryl S-330
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21-Gold (DE3) cells
-
expression in Escherichia coli
expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
-
for expression in Escherichia coli BL21 star DE3 cells
genes pgm1, pgm2, and pgm3, cloning in Escherichia coli strain DH5alpha, expression of His-tagged enzymes in Escherichia coli strain BL21 (DE3)
-
into the vectors pT7BlueT, pBluescript II SK, pTK7, and pET-21a+ for expression in Escherichia coli BL21 star DE3 cells
overexpression in Escherichia coli
-
overexpression in Escherichia coli JM105
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D156A
-
site-directed mutagenesis, the D156A variant displays a dramatically reduced level of phosphorylation of the active site Thr85 compared to the wild-type, and does not acquire phosphatase activity
K240A
-
site-directed mutagenesis, the K240A variant can be phosphorylated by the small molecule activator glucose 1,6-bisphosphate like the wild-type enzyme
T85E
-
site-directed mutagenesis, the T85E variant mimics the active site charge of the activated state of the enzyme, the affinity for activator glucose 1,6-bisphosphate is 4.5fold reduced compared to the wild-type enzyme
T85Q
-
site-directed mutagenesis, the T85Q variant mimics the active site charge of the unactivated state of the enzyme, the affinity for activator glucose 1,6-bisphosphate is only slightly reduced compared to the wild-type enzyme
D156A
-
site-directed mutagenesis, the D156A variant displays a dramatically reduced level of phosphorylation of the active site Thr85 compared to the wild-type, and does not acquire phosphatase activity
-
K240A
-
site-directed mutagenesis, the K240A variant can be phosphorylated by the small molecule activator glucose 1,6-bisphosphate like the wild-type enzyme
-
T85E
-
site-directed mutagenesis, the T85E variant mimics the active site charge of the activated state of the enzyme, the affinity for activator glucose 1,6-bisphosphate is 4.5fold reduced compared to the wild-type enzyme
-
T85Q
-
site-directed mutagenesis, the T85Q variant mimics the active site charge of the unactivated state of the enzyme, the affinity for activator glucose 1,6-bisphosphate is only slightly reduced compared to the wild-type enzyme
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
-
a coupled optical enzyme assay
biotechnology
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