BRENDA - Enzyme Database
show all sequences of 5.4.2.12

Structural role of the active-site metal in the conformation of Trypanosoma brucei phosphoglycerate mutase

Mercaldi, G.F.; Pereira, H.M; Cordeiro, A.T.; Michels, P.A.M.; Thiemann, O.H.; FEBS J. 279, 2012-2021 (2012)

Data extracted from this reference:

Activating Compound
Activating Compound
Commentary
Organism
Structure
additional information
independent on 2,3-bisphosphoglycerate
Trypanosoma brucei
Application
Application
Commentary
Organism
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
Trypanosoma brucei
Cloned(Commentary)
Commentary
Organism
recombinant expression of the His-tagged enzyme in Escherichia coli strain BL21(DE3)
Trypanosoma brucei
Crystallization (Commentary)
Crystallization
Organism
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, 18°C, X-ray diffraction structure determination and analysis at 2.3 A resolution
Trypanosoma brucei
Engineering
Amino acid exchange
Commentary
Organism
D319A
site-directed mutagenesis, substitution of the metal-binding residue Asp319 by Ala results in complete loss of independent PGAM activity
Trypanosoma brucei
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.148
-
3-phospho-D-glycerate
recombinant enzyme, pH 7.4, 37°C
Trypanosoma brucei
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Co2+
two metal sites (M1 and M2) containing cobalt ions are present in the phosphatase domain of the enzyme structure, interaction between Asp319 and the metal bound to the active site, contribution to the domain movement
Trypanosoma brucei
Molecular Weight [Da]
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
56000
-
recombinant enzyme, gel filtration
Trypanosoma brucei
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
2-phospho-D-glycerate
Trypanosoma brucei
-
3-phospho-D-glycerate
-
-
r
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Trypanosoma brucei
Q9NG18
-
-
Purification (Commentary)
Commentary
Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by metal affinity chromatography and gel filtration
Trypanosoma brucei
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2-phospho-D-glycerate
-
727472
Trypanosoma brucei
3-phospho-D-glycerate
-
-
-
r
3-phospho-D-glycerate
-
727472
Trypanosoma brucei
2-phospho-D-glycerate
-
-
-
r
Subunits
Subunits
Commentary
Organism
monomer
1 * 56000, SDS-PAGE, recombinant enzyme
Trypanosoma brucei
More
ligand-induced conformational changes, overview
Trypanosoma brucei
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
37
-
assay at
Trypanosoma brucei
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
19.6
-
3-phospho-D-glycerate
recombinant enzyme, pH 7.4, 37°C
Trypanosoma brucei
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.4
-
assay at
Trypanosoma brucei
Activating Compound (protein specific)
Activating Compound
Commentary
Organism
Structure
additional information
independent on 2,3-bisphosphoglycerate
Trypanosoma brucei
Application (protein specific)
Application
Commentary
Organism
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
Trypanosoma brucei
Cloned(Commentary) (protein specific)
Commentary
Organism
recombinant expression of the His-tagged enzyme in Escherichia coli strain BL21(DE3)
Trypanosoma brucei
Crystallization (Commentary) (protein specific)
Crystallization
Organism
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, 18°C, X-ray diffraction structure determination and analysis at 2.3 A resolution
Trypanosoma brucei
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
D319A
site-directed mutagenesis, substitution of the metal-binding residue Asp319 by Ala results in complete loss of independent PGAM activity
Trypanosoma brucei
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.148
-
3-phospho-D-glycerate
recombinant enzyme, pH 7.4, 37°C
Trypanosoma brucei
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Co2+
two metal sites (M1 and M2) containing cobalt ions are present in the phosphatase domain of the enzyme structure, interaction between Asp319 and the metal bound to the active site, contribution to the domain movement
Trypanosoma brucei
Molecular Weight [Da] (protein specific)
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
56000
-
recombinant enzyme, gel filtration
Trypanosoma brucei
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
2-phospho-D-glycerate
Trypanosoma brucei
-
3-phospho-D-glycerate
-
-
r
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by metal affinity chromatography and gel filtration
Trypanosoma brucei
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2-phospho-D-glycerate
-
727472
Trypanosoma brucei
3-phospho-D-glycerate
-
-
-
r
3-phospho-D-glycerate
-
727472
Trypanosoma brucei
2-phospho-D-glycerate
-
-
-
r
Subunits (protein specific)
Subunits
Commentary
Organism
monomer
1 * 56000, SDS-PAGE, recombinant enzyme
Trypanosoma brucei
More
ligand-induced conformational changes, overview
Trypanosoma brucei
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
37
-
assay at
Trypanosoma brucei
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
19.6
-
3-phospho-D-glycerate
recombinant enzyme, pH 7.4, 37°C
Trypanosoma brucei
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7.4
-
assay at
Trypanosoma brucei
General Information
General Information
Commentary
Organism
evolution
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
Trypanosoma brucei
additional information
ligand-induced conformational changes, overview
Trypanosoma brucei
General Information (protein specific)
General Information
Commentary
Organism
evolution
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
Trypanosoma brucei
additional information
ligand-induced conformational changes, overview
Trypanosoma brucei
KCat/KM [mM/s]
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
3226
-
3-phospho-D-glycerate
recombinant enzyme, pH 7.4, 37°C
Trypanosoma brucei
KCat/KM [mM/s] (protein specific)
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
3226
-
3-phospho-D-glycerate
recombinant enzyme, pH 7.4, 37°C
Trypanosoma brucei
Other publictions for EC 5.4.2.12
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
748541
la Cruz
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Structural characterization, ...
Entamoeba histolytica, Entamoeba histolytica HM1 IMSS
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1705-1716
2018
-
-
1
-
-
-
7
1
-
-
1
4
-
2
-
-
1
-
-
-
-
-
4
1
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-
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1
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1
1
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7
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1
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1
4
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1
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4
1
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-
-
-
-
-
-
-
-
-
-
-
-
-
748833
Singh
Co-factor-independent phospho ...
Leishmania donovani
Parasitology
145
292-306
2018
-
-
1
-
-
-
-
-
1
-
-
2
-
2
-
-
1
-
-
2
-
-
2
1
-
-
-
-
-
-
-
1
-
-
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-
-
1
1
-
-
-
-
-
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1
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2
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1
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2
-
-
2
1
-
-
-
-
-
-
-
-
-
1
1
-
-
-
748834
Tandon
Molecular, biochemical charac ...
Leishmania donovani
Parasitology
145
508-526
2018
-
1
1
-
-
-
2
2
1
-
1
2
-
5
-
-
1
-
-
-
-
-
2
1
-
-
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-
1
-
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1
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2
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1
1
1
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2
2
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2
1
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1
2
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1
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2
1
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-
1
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-
-
-
-
-
-
-
-
747737
Roychowdhury
Complete catalytic cycle of c ...
Staphylococcus aureus, Staphylococcus aureus NCTC 8325
FEBS J.
282
1097-1110
2015
-
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1
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1
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4
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3
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1
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1
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1
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4
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1
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4
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-
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-
-
-
-
-
746646
Roychowdhury
Expression, purification, cry ...
Staphylococcus aureus, Staphylococcus aureus NCTC 8325
Acta Crystallogr. Sect. F
70
53-56
2014
-
-
1
1
-
-
-
-
-
1
-
2
-
3
-
-
1
-
-
-
-
-
2
-
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1
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1
1
1
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1
-
2
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1
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-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
747238
Singh
Cofactor independent phosphog ...
Brugia malayi
BioMed Res. Int.
2014
590281
2014
-
-
1
-
-
-
-
-
-
-
1
2
-
5
-
-
1
-
-
2
-
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2
1
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1
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1
1
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1
2
-
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1
-
2
-
-
2
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
749047
Crowther
Cofactor-independent phosphog ...
Brugia malayi, Caenorhabditis elegans
PLoS Negl. Trop. Dis.
8
e2628
2014
-
-
-
-
-
-
10
2
-
-
-
4
-
7
-
-
-
-
-
4
-
-
4
2
-
-
-
-
-
-
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2
-
-
3
-
-
-
2
-
-
-
3
10
-
2
-
-
-
4
-
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-
-
-
4
-
-
4
2
-
-
-
-
-
-
-
-
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-
-
-
-
-
727472
Mercaldi
Structural role of the active- ...
Trypanosoma brucei
FEBS J.
279
2012-2021
2012
1
1
1
1
1
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1
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1
1
1
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3
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1
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2
2
1
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1
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1
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1
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1
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1
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1
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-
2
2
1
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1
1
-
-
-
-
2
2
-
1
1
716984
Li
Identification and characteriz ...
Dirofilaria immitis, Wolbachia endosymbiont of Dirofilaria immitis, Wolbachia sp.
Vet. Parasitol.
176
350-356
2011
2
-
3
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-
5
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2
2
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4
-
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3
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1
3
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8
2
2
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3
2
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2
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2
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2
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4
2
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6
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2
2
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4
-
1
4
-
8
2
2
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-
4
2
-
-
2
-
-
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-
2
2
728053
Zhao
The glycolytic enzyme, phospho ...
Arabidopsis thaliana
J. Exp. Bot.
62
5179-5189
2011
1
-
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1
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1
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2
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5
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1
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2
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2
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2
4
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734842
Haferkamp
-
Biochemical studies of enzymes ...
Saccharolobus solfataricus, Saccharolobus solfataricus DSM 1617
PH. D. Thesis Universität Duisburg-Essen
2011
0000
2011
-
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1
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6
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1
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2
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1
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4
1
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6
-
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6
6
694538
Foster
The Wolbachia endosymbiont of ...
Wolbachia sp.
Parasitol. Res.
104
1047-1052
2009
-
1
1
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-
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2
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10
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1
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1
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1
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1
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1
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1
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705169
Nowicki
Crystal structures of Leishman ...
Leishmania mexicana
J. Mol. Biol.
394
535-543
2009
-
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1
1
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1
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4
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1
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1
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692403
Saavedra
Glycolysis in Ustilago maydis ...
Ustilago maydis
FEMS Yeast Res.
8
1313-1323
2008
-
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3
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678734
Nukui
Structure and molecular mechan ...
Bacillus anthracis
Biophys. J.
92
977-988
2007
-
-
1
1
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3
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1
1
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2
1
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2
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1
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1
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1
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2
1
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2
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-
679715
Johnsen
Characterization of cofactor-d ...
Archaeoglobus fulgidus, Thermoplasma acidophilum
Extremophiles
11
647-657
2007
2
-
2
-
1
-
1
4
-
2
6
-
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2
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1
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4
2
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3
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1
2
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2
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2
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1
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1
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4
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2
6
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1
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2
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4
2
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3
-
1
2
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-
682237
Djikeng
Cofactor-independent phosphogl ...
Trypanosoma brucei
Parasitol. Res.
100
887-892
2007
-
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1
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2
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1
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1
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Isozymes of phosphoglyceromuta ...
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Singh
Purification and properties of ...
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Purification and properties of ...
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-
-
-
-
-
-
1
-
2
-
-
-
-
-
1
1
-
-
-
-
-
2
-
-
-
-
-
-
-
9
-
2
-
-
-
-
-
-
-
-
-
-
1
-
2
-
-
-
-
-
1
1
-
-
-
-
-
-
-
-
3252
Gatehouse
Phosphoglycerate mutase from w ...
Triticum aestivum
Biochemistry
16
3045-3052
1977
1
-
-
1
-
-
-
-
-
-
2
-
-
2
-
-
1
-
-
1
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
1
-
-
-
1
-
-
-
-
-
-
-
-
2
-
-
-
-
1
-
1
-
1
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
3259
Grisolia
-
Phosphoglycerate mutase from w ...
Oryza sativa, Triticum aestivum
Methods Enzymol.
42
429-435
1975
2
-
-
-
-
-
-
2
-
-
-
-
-
2
-
-
2
-
-
2
1
-
2
-
-
-
-
2
-
-
1
-
-
-
-
2
-
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
2
-
2
1
-
2
-
-
-
-
2
-
-
1
-
-
-
-
-
-
-
3214
Ray
-
Phosphomutases ...
Triticum aestivum
The Enzymes, 3rd Ed. (Boyer, P. D. , ed. )
6
407-477
1972
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
3215
Grisolia
-
Phosphoglyceric acid mutases ...
Triticum aestivum
Methods Enzymol.
5
236-242
1962
-
-
-
-
-
-
1
-
-
-
-
-
-
1
-
-
-
-
-
-
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
-
-
1
1
-
-
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-
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-
-