Information on EC 5.4.2.12 - phosphoglycerate mutase (2,3-diphosphoglycerate-independent)

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

EC NUMBER
COMMENTARY hide
5.4.2.12
-
RECOMMENDED NAME
GeneOntology No.
phosphoglycerate mutase (2,3-diphosphoglycerate-independent)
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2-phospho-D-glycerate = 3-phospho-D-glycerate
show the reaction diagram
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
1-butanol autotrophic biosynthesis (engineered)
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Bifidobacterium shunt
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Biosynthesis of antibiotics
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Biosynthesis of secondary metabolites
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Entner-Doudoroff pathway III (semi-phosphorylative)
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ethylene biosynthesis V (engineered)
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gluconeogenesis I
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gluconeogenesis II (Methanobacterium thermoautotrophicum)
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glycerol degradation to butanol
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Glycine, serine and threonine metabolism
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Glycolysis / Gluconeogenesis
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glycolysis I (from glucose 6-phosphate)
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glycolysis II (from fructose 6-phosphate)
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glycolysis IV (plant cytosol)
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glycolysis V (Pyrococcus)
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Metabolic pathways
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Methane metabolism
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Microbial metabolism in diverse environments
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photosynthetic 3-hydroxybutanoate biosynthesis (engineered)
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Rubisco shunt
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superpathway of glucose and xylose degradation
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Entner Doudoroff pathway
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glycolysis
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SYSTEMATIC NAME
IUBMB Comments
D-phosphoglycerate 2,3-phosphomutase (2,3-diphosphoglycerate-independent)
The enzymes from higher plants, algae, fungi, nematodes, sponges, coelenterates, myriapods, arachnids, echinoderms, archaea and some bacteria (particularly Gram-positive) have maximum activity in the absence of 2,3-bisphospho-D-glycerate. cf. EC 5.4.2.11 phosphoglycerate mutase (2,3-diphosphoglycerate-dependent). The enzyme contains two Mn2+ (or in some species two Co2+ ions). The reaction involves a phosphotransferase reaction to serine followed by transfer back to the glycerate at the other position. Both metal ions are involved in the reaction.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
cofactor-independent isoform
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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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SwissProt
Manually annotated by BRENDA team
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Uniprot
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
rice
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-
Manually annotated by BRENDA team
almond
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-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
strain OT3
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-
Manually annotated by BRENDA team
strain OT3
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-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
potato
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-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
cofactor-dependent isoform
Uniprot
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
mung bean
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-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
additional information
by sequence alignment found in Arabidopsia thaliana, Oryza sativa, Anthithamnion sp., Escherichia coli, Bacillus subtilis, Bacillus megaterium, Caenorhabditis elegans
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
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PGAMs that are dependent on (EC 5.4.2.11) or independent of the 2,3-bisphosphoglycerate cofactor are members of two distinct protein families
malfunction
PMG1/PMG2 double mutants have no detectable iPGAM activity and show defects in blue light-, abscisic acid-, and low CO2-regulated stomatal movements. Vegetative plant growth is severely impaired in the double mutants and pollen is not produced, phenotypes, overview; PMG1/PMG2 double mutants have no detectable iPGAM activity and show defects in blue light-, abscisic acid-, and low CO2-regulated stomatal movements. Vegetative plant growth is severely impaired in the double mutants and pollen is not produced, phenotypes, overview
physiological function
2,3-biphosphoglycerate-independent phosphoglycerate mutase is a key enzymatic activity in glycolysis and catalyses the reversible interconversion of 3-phosphoglycerate to 2-phosphoglycerate, functions of iPGAMs and glycolysis in stomatal function and plant growth, overview. Both isozymes PMG1 and PMG2 and glycolytic activity are critical for guard cell function and fertility; 2,3-biphosphoglycerate-independent phosphoglycerate mutase is a key enzymatic activity in glycolysis and catalyses the reversible interconversion of 3-phosphoglycerate to 2-phosphoglycerate, functions of iPGAMs and glycolysis in stomatal function and plant growth, overview. Both isozymes PMG1 and PMG2 and glycolytic activity are critical for guard cell function and fertility
additional information
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ligand-induced conformational changes, overview
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-phospho-D-glycerate
3-phospho-D-glycerate
show the reaction diagram
2-Phosphoglycerate
3-Phosphoglycerate
show the reaction diagram
3-phospho-D-glycerate
2-phospho-D-glycerate
show the reaction diagram
3-Phosphoglycerate
2-Phosphoglycerate
show the reaction diagram
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-phospho-D-glycerate
3-phospho-D-glycerate
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
-
1 mm, 19% of activity with 0.5 mM Mn2+
Cd2+
-
divalent cation required for activity
CoCl2
inhibition by EDTA is reversible by incubation with CoCl2, but not MnCl2, FeSO4, CuSo4, NiCl2, ZnCl2
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,10-phenanthroline
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2,3-Butanedione
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8-hydroxyquinoline 5-sulfonic acid
diethyl dicarbonate
irreversible inhibition, saturating concentrations of substrate protect
iodoacetate
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N-ethylmaleimide
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p-mercuribenzoate
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phosphate
100 mM, 70% residual activity
Sodium metavanadate
vanadate
up to 0.1 mM, 90% maximal inhibition. Inhibition may be partially reversed by EDTA
additional information
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2,3-bisphosphoglycerate
2,3-diphosphoglycerate
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.066 - 1.1
2-phospho-D-glycerate
0.06 - 1.47
2-phosphoglycerate
4.4
2-[5-Amino-2-(4-fluoro-phenyl)-6-oxo-6H-pyrimidin-1-yl]-N-(1-benzyl-2-oxo-2-thiazol-2-yl-ethyl)-acetamide
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pH 7.4, 1 mM Mn2+
0.04 - 5.2
3-phospho-D-glycerate
0.324 - 1.1
3-phosphoglycerate
additional information
additional information
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.04 - 199
2-phospho-D-glycerate
1.51 - 434
3-phospho-D-glycerate
additional information
additional information
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
7.84 - 36.45
2-phospho-D-glycerate
1023
19.81 - 3226
3-phospho-D-glycerate
201
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3.3
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pH 7.0, 50C
40
pH 7.0, 30C, formation of 2-phospho-D-glycerate
72
pH 7.0, 30C, formation of 3-phospho-D-glycerate
83.8
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plastidic enzyme
93
pH 7.0, 30C, formation of 2-phospho-D-glycerate
202.5
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-
225
in 30 mM Tris-HCl, 5 mM MgSO4, 20 mM KCl, pH 7.5, at 30C; purified recombinant His-tagged enzyme, pH 7.5, 30C
256
pH 7.0, 30C, formation of 3-phospho-D-glycerate
419
formation of 2-phospho-D-glycerate, pH 7.6, 25C
500
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selenomethionyl-phosphoglycerate mutase
622.5
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cytosolic enzyme
1500
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methionyl-phosphoglycerate mutase
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.8 - 6.2
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formation of 2-phospho-D-glycerate
7.3
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plastidic enzyme, substrate 2-phosphoglycerate
7.4
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assay at
7.5 - 7.8
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7.5 - 8.2
for both directions of reaction
7.7 - 8.3
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7.8
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6
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about 40% of maximal activity
6 - 8
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24% and 36% of maximal activity at pH 6.0 and pH 7.0 in the presence of 1 mM and 0.5 mM Mn2+, respectively
6 - 8.1
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6 - 8.7
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less than 50% of maximal activity above and below
6.8 - 8.8
more than 75% of maximum activity within this range, formation of 2-phospho-D-glycerate
7.7
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about 70% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
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assay at
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5
-
predicted from amino acid sequence
6
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isoelectric focusing
6.3
calculated from amino acid sequence
7.4
calculated from amino acid sequence
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
guard cell proteome, overview; guard cell proteome, overview
Manually annotated by BRENDA team
additional information
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optimal enzyme production at 37C
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
23800
2 * 23800, calculated, 2 * 24000, SDS-PAGE
24000
2 * 23800, calculated, 2 * 24000, SDS-PAGE
26000
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2 * 26000, SDS-PAGE
44100
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1 * 44100, calculated, 1 * 48000, SDS-PAGE of His-tagged protein
45179
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x * 45179, deduced from nucleotide sequence
45200
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4 * 45200, deduced from nucleotide sequence
45300
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4 * 45300, deduced from nucleotide sequence
46800
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x * 46000-48000, SDS-PAGE, x * 46800, calculated
48000
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1 * 44100, calculated, 1 * 48000, SDS-PAGE of His-tagged protein
50000 - 60000
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gel filtration, SDS-PAGE
52000
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gel filtration
54000
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sedimentation equilibrium centrifugation
57000
x * 57000, calculated from amino acid sequence
58000
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gel filtration
60557
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1 * 60557, deduced from nucleotide sequence
60724
x * 60724, calculated, x * 60000, recombinant protein with His-tag, SDS-PAGE
61000
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gel filtration, SDS-PAGE
63500
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plastidic enzyme, gel filtration
64000
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gel filtration, SDS-PAGE
64500
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cytosolic enzyme, gel filtration
100000
around 100000 Da, SDS-PAGE, enzyme fused with N-terminal maltose binding protein
183500
-
gel filtration
190600
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
tetramer
additional information
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ligand-induced conformational changes, overview
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphoprotein
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autophosphorylation at Ser59
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
protein is composed of two structural and functiional domains, the phosphatase and the transferase. Comparison with the structurally similar domains of in Bacillus stearothermophilus
crystals of iPGM complexed with 3-phosphoglycerate and Mn2+ at 1.9 A resolution
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crystals of wild-type and S62A mutant at 1.4 A resolution
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methionyl and selenomethionyl phosphoglycerate mutase, vapor drop hanging diffusion, mixing equal volumes of protein solution, i.e. 50 mg/ml protein in 150 mM 3-phosphoglycerate, pH 7.4 and reservoir solution containing 2 M ammonium sulfate, 25 mM zinc acetate, 20 mM cesium chloride, 15 mM 2-mercaptoethanol, 3% polyethylene glycol 200 and 50 mM Tris-HCl, pH 7.4, crystals diffract to 2.5 A resolution
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crystals of iPGAM complexed with 3-phosphoglycerate and Co2+, hanging-drop vapor diffusion, crystallization drops contain equal volumes of reservoir and enzyme solution, 5 mg/ml iPGAM, 1.5 mM 3-phosphoglycerate, 50 mM NaCl, 0.01 mM CoCl2 in 20 mM TEA buffer, pH 7.4, crystals diffract to 1.9 A
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iPGAM crystallized with 3-phosphoglycerate or 2-phosphoglycerate at high and low cobalt concentrations (4 mM and 0.01 mM), hanging drop vapor diffusion method, using 0.08 M ammonium acetate, 0.04 M trisodium citrate dihydrate pH 6.0, and 24% (w/v) PEG 4000
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space group R32, resolution of 2.2 A
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purified recombinant His-tagged enzyme, hanging drop vapour diffusion method, mixing of 0.003 ml of 8 mg/ml protein solution containing 20 mM Tris-acetate-EDTA, pH 7.4, 50 mM NaCl, 001 mM CoCl2, with 0.003 ml of reservoir solution containing 0.05 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.1, and 25% w/v PEG 3350, 18C, X-ray diffraction structure determination and analysis at 2.3 A resolution
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 9.5
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3259
5.5
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8 h, 4C, complete inactivation
3243
6 - 10
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3252
6.8
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rapid inactivation
3243
11
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24 h, 4C, 15% loss of activity
3243
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
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plastidic enzyme: 50 min, 50% loss of activity, cytosolic enzyme: 125 min, 50% loss of activity, no protection by 2-phosphoglycerate, 3-phosphoglycerate, 2,3-bisphosphoglycerate, phosphate
70
-
half-life 150 min in presence of Mn2+ and Mg2+. Half-life 30 min in the absence of Mn2+ and Mg2+
85
-
half-life 15 min in presence of Mn2+ and Mg2+
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
PMSF increases the stability during purification procedure
-
rapid decrease in activity when no stabilizer is added. In presence of NaCl, CoCl2, and imidazole, stable for 1 month at 4C
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, 10 mM Tris-HCl buffer, pH 8.0
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-20C, 50% v/v glycerol, less than 50% loss of activity in 2 months
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-20C, 6 months, 10% loss of activity
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-20C, potassium phosphate buffer, pH 7.2, 20-25% glycerol, 1 month, no loss of activity
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0-4C, ammonium sulfate suspension, pH 7.2
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
amylose column chromatography
HiTrap nickel chelating column chromatography and HiTrap Q column chromatography
HiTrap nickel chelating column chromatography and HiTrap Q column chromatography; recombinant His6-tagged enzyme from Escherichia coli strain C2566/T7 by nickel affinity chromatography, dialysis and anion exchange chromatography
metal affinity Talon column chromatography
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partially purified
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partialy purified
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by metal affinity chromatography and gel filtration
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recombinant His6-tagged enzyme from Escherichia coli strain C2566/T7 by nicke affinity chromatography, dialysis and anion exchange chromatography
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recombinant iPGAM
recombinant iPGM
recombinant phosphoglycerate mutase
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recombinant protein
recombinant protein expressed in Escherichia coli
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli (inactive unsoluble protein) and Kluyveromyces lactis (active enzyme)
expressed in Escherichia coli C2566/T7 cells
expressed in Escherichia coli C2566/T7 cells; expression of C-terminally His6-tagged enzyme in Escherichia coli strain C2566/T7
expression in Escherichia coli
expression in Escherichia coli with C-terminal His-tag
expression in Escherichia coli with His-tag
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expression in Escherichia coli with His6-tag
expression in Escherichia coli; expression in Escherichia coli
expression of C-terminally His-tagged enzyme in Escherichia coli strain C2566/T7
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expression of native and selenomethionyl phosphoglycerate mutase in Escherichia coli
-
His-tagged enzyme is expressed in Escherichia coli BL21 cells
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recombinant expression of the His-tagged enzyme in Escherichia coli strain BL21(DE3)
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H123N
-
3% of wild-type activity
H125N
-
67% of wild-type activity
H128N
-
20% of wild-type activity
H42N
-
91% of wild-type activity
H42N/H128N
-
8% of wild-type activity
H445N
-
18% of wild-type activity
H462N
-
0.3% of wild-type activity
H66N
-
2% of wild-type activity
H23A
no enzymic activity. Like wild-type, mutant forms a dimer
D319A
-
site-directed mutagenesis, substitution of the metal-binding residue Asp319 by Ala results in complete loss of independent PGAM activity
additional information
Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
inactivation by EDTA is reversible by incubation with CoCl2, but not MnCl2, FeSO4, CuSo4,NiCl2, ZnCl2
inhibition of enzyme by vanadate may be partially reversed by EDTA
metal ions do not reactivate the enzyme after denaturation with guanidine-HCl
reactivation of EDTA-treated enzyme by Mn2+. Several activation-deactivation cycles can be elicited
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
drug development
-
TbiPGAM is an attractive molecular target for drug development, the apoenzyme conformation described here provides opportunities for its use in structure-based drug design approaches
medicine
drug target for novel anti-filarial therapies that selectively target the Wolbachia endosymbiont of Brugia malayi
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