Information on EC 5.4.2.11 - phosphoglycerate mutase (2,3-diphosphoglycerate-dependent)

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

EC NUMBER
COMMENTARY hide
5.4.2.11
-
RECOMMENDED NAME
GeneOntology No.
phosphoglycerate mutase (2,3-diphosphoglycerate-dependent)
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
2-phospho-D-glycerate = 3-phospho-D-glycerate
show the reaction diagram
[enzyme]-L-histidine + 2,3-bisphospho-D-glycerate = [enzyme]-Ntau-phospho-L-histidine + 2/3-phospho-D-glycerate
show the reaction diagram
(1a)
-
-
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[enzyme]-L-histidine + 2,3-bisphospho-D-glycerate = [enzyme]-Ntau-phospho-L-histidine + 3-phospho-D-glycerate
show the reaction diagram
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-
-
-
[enzyme]-Ntau-phospho-L-histidine + 2-phospho-D-glycerate = [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate
show the reaction diagram
(1b)
-
-
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[enzyme]-Ntau-phospho-L-histidine + 2/3-bisphospho-D-glycerate = [enzyme]-L-histidine + 2,3-bisphospho-D-glycerate
show the reaction diagram
(1d)
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biosynthesis of antibiotics
-
-
Biosynthesis of secondary metabolites
-
-
formaldehyde assimilation I (serine pathway)
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-
gluconeogenesis III
-
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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 III (from glucose)
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heterolactic fermentation
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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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Entner Doudoroff pathway
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glycolysis
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SYSTEMATIC NAME
IUBMB Comments
D-phosphoglycerate 2,3-phosphomutase (2,3-diphosphoglycerate-dependent)
The enzymes from vertebrates, platyhelminths, mollusks, annelids, crustaceans, insects, algae, fungi, yeast and some bacteria (particularly Gram-negative) require 2,3-bisphospho-D-glycerate as a cofactor. The enzyme is activated by 2,3-bisphospho-D-glycerate by transferring a phosphate to histidine (His10 in man and Escherichia coli, His8 in Saccharomyces cerevisiae). This phosphate can be transferred to the free OH of 2-phospho-D-glycerate, followed by transfer of the phosphate already on the phosphoglycerate back to the histidine. cf. EC 5.4.2.12 phosphoglycerate mutase. The enzyme has no requirement for metal ions. This enzyme also catalyse, slowly, the reactions of EC 5.4.2.4 bisphosphoglycerate mutase.
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
bovine
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
X
-
-
Manually annotated by BRENDA team
X
-
-
Manually annotated by BRENDA team
AM1
-
-
Manually annotated by BRENDA team
AM1
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
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-phospho-D-glycerate
3-phospho-D-glycerate
show the reaction diagram
2-phospho-D-glycerate + 2,3-bisphosphoglycerate
3-phospho-D-glycerate + 2,3-bisphosphoglycerate
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
3-Phosphoglycerate
?
show the reaction diagram
Hydroxypyruvic acid 3-phosphate
?
show the reaction diagram
additional information
?
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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
2-phospho-D-glycerate + 2,3-bisphosphoglycerate
3-phospho-D-glycerate + 2,3-bisphosphoglycerate
show the reaction diagram
-
-
-
r
2-Phosphoglycerate
3-Phosphoglycerate
show the reaction diagram
-
-
-
r
3-Phosphoglycerate
?
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2,3-bisphosphoglycerate
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required to prime the reaction in an initial phosphorylation step
2,3-bisphosphoglyceric acid
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dependent on 2,3-bisphosphoglyceric acid for activity
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1-benzyl 4-[(3R,4R,6R)-6-[1-(hex-5-ynoyloxy)-1-methylethyl]-1-oxaspiro[2.5]oct-4-yl] (2R)-2-(2,3-dihydro-1H-indol-3-ylmethyl)butanedioate
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i.e. MJE3, spiroepoxide with anti-proliferative effects in human breast cancer cells. MJE3 covalently inactiviates enzyme at K100
2,3-Butanedione
benzene hexacarboxylate
benzene-1,2,3-tricarboxylate
benzene-1,2,4,5-tetracarboxylate
benzene-1,2,4-tricarboxylate
benzene-1,3,5-tricarboxylate
diethyldicarbonate
Inositol hexakisphosphate
metavanadate
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less than 5% residual activity at 10 mM after 10 min incubation
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N-Bromoacetylethanolamine
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Sodium metavanadate
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tetrathionate
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inactivation of MM-type isozyme, 50% of MB-type, BB-type not affected
Trinitrobenzenesulfonate
vanadate
acting as a substrate mimic, enzyme binding structure, overview
additional information
-
not Mg2+
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2,3-bisphosphoglycerate
2,3-diphosphoglycerate
2-phosphoglycollate
2-phosphohydroxypyruvate
-
30fold activation of phosphatase activity
Co2+
phosphoglycerate mutase is upregulated in the cobalt-treated mouse cerebrum
additional information
phosphoglycerate mutase activity increases by peony root extract administration
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.041 - 0.69
2-phosphoglycerate
0.22 - 1.43
3-phospho-D-glycerate
0.026 - 7.46
3-phosphoglycerate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0009 - 3200
3-phospho-D-glycerate
0.078 - 530
3-phosphoglycerate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.006 - 0.022
benzene hexacarboxylate
0.023 - 0.067
benzene-1,2,3-tricarboxylate
0.013 - 0.055
benzene-1,2,4,5-tetracarboxylate
0.021 - 0.062
benzene-1,2,4-tricarboxylate
0.024 - 0.053
benzene-1,3,5-tricarboxylate
0.004 - 0.035
Inositol hexakisphosphate
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.5
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glioblastoma
0.56
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anaplastic astrocytoma
0.67
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meningioma
0.7
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astrocytoma
1.5
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brain, normal tissue
20.03
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218
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recombinant enzyme
515
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-
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.8
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7 - 7.6
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 8
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less than 50% of maximal activity above and below
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5
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isoelectric focusing
6.6
isoelectric focusing
6.7
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calculated from amino acid sequence
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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capillary and artery endothelia of the brain, liver and kidney
Manually annotated by BRENDA team
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increase in enzyme activity and mRNA level after application of triiodothyronine or induction of hypoxia by 90% nitrogen/10% oxygen. Propylthiouracil produces decrease in enzyme activity
Manually annotated by BRENDA team
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increase in enzyme activity and mRNA level after application of triiodothyronine or induction of hypoxia by 90% nitrogen/10% oxygen. Propylthiouracil produces decrease in enzyme activity
Manually annotated by BRENDA team
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the serum of healthy persons contains BB-type isozyme, whereas in patients with Duchenne muscular dystrophy it contains MM-type isozyme
Manually annotated by BRENDA team
additional information
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in early fetal life PGAM-BB is the only isozyme present in all tissues, in myogenesis these phenotypes undergo transition to MM-type via a MB-hybrid
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
additional information
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not in mitochondria, lysosomes, or other cytoplasmic organelles
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Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Burkholderia pseudomallei (strain 1710b)
Burkholderia pseudomallei (strain 1710b)
Burkholderia pseudomallei (strain 1710b)
Burkholderia pseudomallei (strain 1710b)
Burkholderia pseudomallei (strain 1710b)
Burkholderia pseudomallei (strain 1710b)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Neisseria gonorrhoeae (strain NCCP11945)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
21948
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2 * 21948, calculated
23668
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4 * 23678, chromosomal enzyme, 4 * 23669, mutants H196Q and H151Q, 4 * 23668, mutant H163Q, mass spectrometry
23669
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4 * 23678, chromosomal enzyme, 4 * 23669, mutants H196Q and H151Q, 4 * 23668, mutant H163Q, mass spectrometry
23678
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4 * 23678, chromosomal enzyme, 4 * 23669, mutants H196Q and H151Q, 4 * 23668, mutant H163Q, mass spectrometry
26000
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2 * 26000, calculated from amino acid sequence
28000
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4 * 28000, SDS-PAGE
28680
calculated from amino acid sequence; calculated from amino acid sequence
28900
-
calculated from amino acid sequence
28940
deduced from amino acid sequence
30500
gel filtration
46700
-
dynamic light scattering
56000
-
gel filtration
56300
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sedimentation equilibrium centrifugtion
57000
-
gel filtration
60000
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MM-type isozyme in nucleus and cytoplasm, gel filtration
102000
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gel filtration
120000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homotetramer
tetramer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified recombinant His-tagged enzyme, in apoform or complexed with 2-phosphoserine, with vanadate + 3-phosphoglycerate, with vanadate + glycerol, with 2,3-bisphosphoglycerate + 3-phosphoglycerate, or with malonate, sitting-drop vapour diffusion by mixing 0.0004 ml reservoir solution with 0.0004 ml protein solution, containing 25 mM HEPES, pH 7.0, 500 mM NaCl, 5% v/v glycerol, 0.025% w/v sodium azide and 2 mM DTT, over a reservoir volume of 0.08 ml, the reservoir solution, containing 5% PEG 1000, 10% glycerol, 30% PEG 600, and 100 mM MES pH 7.5, is supplemented with the ligands at different concentrations, X-ray diffraction structure determination and analysis at 1.5-2.25 A resolution, molecular replacement and modeling
crystals of phosphohistidine activated dPGM are grown from hanging drops from a protein solution containing 15 mg/ml dPGM in 20 mM Tris-HCl, pH 8.0, with 100 mM NaCl and a reservoir comprising 100 mM Tris-HCl, pH 8.75, 200 mM Li2SO4 and 20% polyethylene glycol 4000, crystals diffrakt to 1.25 A resolution
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in complex with citrate, heterodimer structure of phosphoglycerate mutase/bisphosphoglycerate mutase
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modeling study of enzyme in complex with inhibitor 1-benzyl 4-[(3R,4R,6R)-6-[1-(hex-5-ynoyloxy)-1-methylethyl]-1-oxaspiro[2.5]oct-4-yl] (2R)-2-(2,3-dihydro-1H-indol-3-ylmethyl)butanedioate
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C-terminal phosphoglycerate mutase domain of mouse Sts-1, crystallization in space group C2 with two different crystal forms. Data of native and selenomethionine protein
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both native and selenomethionine-labelled protein
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recombinant protein with His6-tag
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crystal structure at 2.12 a resolution
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crystal structure; sitting drop method, equal volumes of protein solution at a concentration of 10 mg/ml and well solution are mixed, well solution contains 60 mM Tris-HCl, pH 8.65, 120 mM lithium sulfate and 22-24% polyethylene glycol 4000, protein solution contains 1 mM inositol hexakisphosphate, crystals diffract to 2.3 A resolution
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crystallization of PGAM complexed with inositol hexakisphosphate and benzene hexacarboxylate, crystal structures at 2.5-2.8 A resolution
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hanging drop, 10 mg/ml ScPGM, 55% ammonium sulfate in 10 mM imidazole buffer, pH 6.8, 1 mM 3-phosphoglycerate, crystals of ScPGM complexed with 3-phosphoglycerate diffract to 1.7 A
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45
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wild-type, 1 h, 10% loss of activity, mutant M230I, 20 min, 50% loss of activity, 1 h, 90% loss of activity. In presence of 2,3-bisphosphoglycerate, both forms remain stable
55 - 60
additional information
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
little effect of the protease thermolysin on enzyme activity
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loss of 45% of mutase activity after treatment with thermolysin
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relatively resistant to short periods of treatment with thermolysin, both mutase and phosphatase activity decline at the same rate, approx. 40% loss of activity after 120 min treatment with thermolysin
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unstable to 8 M urea
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 10 mM sodium phosphate buffer, pH 7.0, 5 mM MgCl2, 2 mM 2-mercaptoethanol, 10% loss of activity in 1 week
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-20°C, 10 mM sodium phosphate buffer, pH 7.0, 5 mM MgCl2, 2 mM 2-mercaptoethanol, 13% loss of activity in 1 week
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4°C, saturated ammonium sulfate, pH 7.0, at least 1 month stable
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
additional activities: bisphosphoglyceromutase, 2,3-diphosphoglycerophosphatase
-
additional activity: 2,3-diphosphoglycerate phosphatase
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ammonium sulfate, CM cellulose, Superose 12
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erythrocytes, enzyme has activities of bisphosphoglyceromutase and bisphosphoglycerate phosphatase
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MM-type isozyme and M-subunit from skeletal muscle, BB-type isozyme and B-subunit from brain
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MM-type isozyme of muscle
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MM-type, BB-type, MB-type isozymes, these enzymes also show glycerate 2,3-diphosphate synthase and glycerate 2,3-diphosphate phosphatase activity
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recombinant dPGM
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recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3)-R3-pRARE2 cells by nickel affinity chromatography and gel filtration
recombinant PGAM
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recombinant protein with His6-tag
-
recpmbinant PGAM
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
C-terminal phosphoglycerate mutase domain of mouse Sts-1, Sts-1PGM, comprised of residues 369-640 and an N-terminal His-tag
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expressed in PK-15 cells; expressed in PK-15 cells
expressed in Saccharomyces cerevisiae
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expression in Escherichia coli
expression in Escherichia coli with His6-tag
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expression in Escherichia coli wtih N-terminal His6-tag
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expression in Saccharomyces cerevisiae
isozyme PGAM-B
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isozyme PGAM-M
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overexpression in Saccharomyces cerevisae
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recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)-R3-pRARE2 cells
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K100A
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no covalent modification by inhibitor 1-benzyl 4-[(3R,4R,6R)-6-[1-(hex-5-ynoyloxy)-1-methylethyl]-1-oxaspiro[2.5]oct-4-yl] (2R)-2-(2,3-dihydro-1H-indol-3-ylmethyl)butanedioate
A60S
-
69% of wild-type activity
E86Q
-
1% of wild-type activity
H181A
-
His181 is substituted by Ala in site-directed mutagenesis. The resulting enzyme has a reduced activity and still requires 2,3-diphosphoglycerate. His181 seems to be important for cofactor-binding
K246G
-
mutant enzymes in which Ser11 is replaced by Gly, i.e. S11G and Lys246 by Gly, i.e. K246G do not have significantly altered kinetic values
L245G
-
39% of wild-type mutase activity, 111% of wild-type phosphatase activity
L245G/L246G
-
105% of wild-type mutase activity, 111% of wild-type phosphatase activity
L246G
-
98% of wild-type mutase activity, 122% of wild-type phosphatase activity
S11A
-
4% of wild-type activity
S11G
-
mutant enzymes in which Ser11 is replaced by Gly, i.e. S11G and Lys246 by Gly, i.e. K246G do not have significantly altered kinetic values
R120Q
-
59% of wild-type activity
R120Q/R121Q
-
62% of wild-type activity
R121Q
-
12% of wild-type activity
R14Q
-
less than 1% of wild-type activity
R94Q
-
1% of wild-type activity
S62A
-
loss of activity during purification
Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
renatured after denaturation with guanidine-HCl
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
drug development
medicine
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