BRENDA - Enzyme Database
show all sequences of 5.1.1.13

Crystal structure of a pyridoxal 5'-phosphate-dependent aspartate racemase derived from the bivalve mollusc Scapharca broughtonii

Mizobuchi, T.; Nonaka, R.; Yoshimura, M.; Abe, K.; Takahashi, S.; Kera, Y.; Goto, M.; Acta Crystallogr. Sect. F 73, 651-656 (2017)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
Scapharca broughtonii
Crystallization (Commentary)
Crystallization
Organism
purified recombinant His-tagged enzyme, hanging drop vapour diffusion method, mixing of 0.006 ml of 2.5 mg/ml protein in 10 mM Tris-HCl, 20 mM pyridoxal 5'-phosphate, 1 mM 2-mercaptoethanol, pH 8.8, with 0.003 ml of reservoir solution containing 27% w/v PEG 4000, 50 mM sodium acetate, pH 5.0, 200 mM ammonium acetate, and 15% v/v glycerol, and equilibration against 0.1 ml of reservoir solution, 14°C, X-ray diffraction structure determination and analysis at 1.90 A resolution
Scapharca broughtonii
Inhibitors
Inhibitors
Commentary
Organism
Structure
malonate
-
Scapharca broughtonii
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
L-aspartate
Scapharca broughtonii
-
D-aspartate
-
-
r
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Scapharca broughtonii
-
-
-
Purification (Commentary)
Commentary
Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
Scapharca broughtonii
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
L-aspartate
-
746669
Scapharca broughtonii
D-aspartate
-
-
-
r
additional information
SbAspR catalyzes both racemization and dehydration. Residue Arg140 recognizes the beta-carboxyl group of the substrate aspartate in SbAspR
746669
Scapharca broughtonii
?
-
-
-
-
Cofactor
Cofactor
Commentary
Organism
Structure
pyridoxal 5'-phosphate
dependent on
Scapharca broughtonii
Cloned(Commentary) (protein specific)
Commentary
Organism
recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3)
Scapharca broughtonii
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
pyridoxal 5'-phosphate
dependent on
Scapharca broughtonii
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant His-tagged enzyme, hanging drop vapour diffusion method, mixing of 0.006 ml of 2.5 mg/ml protein in 10 mM Tris-HCl, 20 mM pyridoxal 5'-phosphate, 1 mM 2-mercaptoethanol, pH 8.8, with 0.003 ml of reservoir solution containing 27% w/v PEG 4000, 50 mM sodium acetate, pH 5.0, 200 mM ammonium acetate, and 15% v/v glycerol, and equilibration against 0.1 ml of reservoir solution, 14°C, X-ray diffraction structure determination and analysis at 1.90 A resolution
Scapharca broughtonii
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
malonate
-
Scapharca broughtonii
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
L-aspartate
Scapharca broughtonii
-
D-aspartate
-
-
r
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
Scapharca broughtonii
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
L-aspartate
-
746669
Scapharca broughtonii
D-aspartate
-
-
-
r
additional information
SbAspR catalyzes both racemization and dehydration. Residue Arg140 recognizes the beta-carboxyl group of the substrate aspartate in SbAspR
746669
Scapharca broughtonii
?
-
-
-
-
General Information
General Information
Commentary
Organism
additional information
residue Arg140 recognizes the beta-carboxyl group of the substrate aspartate in SbAspR. The aromatic proline interaction between the domains, which favours the closed form of SbAspR, might influence the arrangement of Arg140 at the active site, active site structure of SbAspR, overview
Scapharca broughtonii
physiological function
the enzyme is responsible for D-aspartate biosynthesis in vivo. Enzyme SbAspR is a type II PLP-dependent enzyme. D-Aspartate is one of the most abundant free D-amino acids present in the nervous and reproductive systems and plays important physiological roles, including regulating developmental processes, hormone secretion and steroidogenesis
Scapharca broughtonii
General Information (protein specific)
General Information
Commentary
Organism
additional information
residue Arg140 recognizes the beta-carboxyl group of the substrate aspartate in SbAspR. The aromatic proline interaction between the domains, which favours the closed form of SbAspR, might influence the arrangement of Arg140 at the active site, active site structure of SbAspR, overview
Scapharca broughtonii
physiological function
the enzyme is responsible for D-aspartate biosynthesis in vivo. Enzyme SbAspR is a type II PLP-dependent enzyme. D-Aspartate is one of the most abundant free D-amino acids present in the nervous and reproductive systems and plays important physiological roles, including regulating developmental processes, hormone secretion and steroidogenesis
Scapharca broughtonii
Other publictions for EC 5.1.1.13
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)
746669
Mizobuchi
Crystal structure of a pyrido ...
Scapharca broughtonii
Acta Crystallogr. Sect. F
73
651-656
2017
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1
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2
2
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746724
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Acropora millepora, Crassostrea gigas, Penaeus monodon
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3
-
6
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13
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4
-
10
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3
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9
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3
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10
3
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6
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13
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4
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3
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9
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3
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10
3
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9
9
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10
10
747720
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Picrophilus torridus, Picrophilus torridus ATCC 700027 / DSM 9790 / JCM 10055 / NBRC 100828
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20
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2016
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1
1
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2
1
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4
-
5
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1
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10
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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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10
1
1
1
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1
1
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1
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1
1
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747721
Washio
Molecular cloning and enzymol ...
Thermococcus litoralis, Thermococcus litoralis ATCC 51850 / DSM 5473 / JCM 8560 / NS-C
Extremophiles
20
711-721
2016
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1
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3
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11
3
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1
1
2
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6
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1
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1
3
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8
1
1
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1
2
1
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1
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1
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3
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11
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3
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1
1
2
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1
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1
3
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8
1
1
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1
2
1
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1
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2
2
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2
2
746649
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Acta Crystallogr. Sect. F
71
1012-1016
2015
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1
1
1
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4
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1
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1
1
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746719
Tanaka-Hayashi
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Mus musculus
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47
79-86
2015
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1
-
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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1
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1
1
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1
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1
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2
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1
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2
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3
-
1
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1
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3
3
-
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-
746721
Matsuda
Biosynthesis of D-aspartate i ...
Homo sapiens, Rattus norvegicus
Amino Acids
47
975-985
2015
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2
-
2
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2
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6
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3
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2
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4
4
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748452
Katane
A sensitive assay for measuri ...
Streptococcus thermophilus
J. Pharm. Biomed. Anal.
116
109-115
2015
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1
1
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1
1
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1
1
716952
Zhang
-
QM/MM study on catalytic mecha ...
Pyrococcus horikoshii, Pyrococcus horikoshii OT-3
Theoret. Chem. Accounts
129
781-791
2011
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1
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44
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4
1
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1
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1
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1
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4
1
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728034
Ohide
D-Amino acid metabolism in mam ...
Mus musculus, Rattus norvegicus
J. Chromatogr. B
879
3162-3168
2011
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2
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6
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22
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2
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2
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22
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2
2
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1
1
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706558
Kim
Aspartate racemase, generating ...
Mus musculus
Proc. Natl. Acad. Sci. USA
107
3175-3179
2010
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1
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1
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15
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1
1
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1
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15
1
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1
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2
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706688
Topo
The role and molecular mechani ...
Rattus norvegicus
Reprod. Biol. Endocrinol.
7
120-130
2009
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6
1
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1
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1
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1
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695052
Ohtaki
Structure of aspartate racemas ...
Pyrococcus horikoshii, Pyrococcus horikoshii OT-3
Proteins Struct. Funct. Bioinform.
70
1167-1174
2008
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1
1
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1
1
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3
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2
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662507
Spinelli
D-aspartic acid in the nervous ...
Aplysia limacina
J. Cell. Physiol.
206
672-681
2006
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674359
Abe
Cloning and expression of the ...
Scapharca broughtonii
J. Biochem.
139
235-244
2006
2
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1
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1
2
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4
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1
1
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660993
D'Aniello
Cephalopod vision involves dic ...
Sepia officinalis
Biochem. J.
386
331-340
2005
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662506
Raucci
D-Aspartate modulates transcri ...
Pelophylax esculentus
J. Cell. Physiol.
204
445-454
2005
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661647
Yamashita
Molecular identification of mo ...
Bifidobacterium bifidum, Bifidobacterium bifidum NBRC 14252
Eur. J. Biochem.
271
4798-4803
2004
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1
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5
2
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2
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5
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1
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1
1
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1
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1
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1
1
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5
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2
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2
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1
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1
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2
1
1
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2
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1
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1
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649759
Sielaff
The mcyF gene of the microcyst ...
Microcystis aeruginosa
Biochem. J.
373
909-916
2003
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1
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5
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1
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1
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1
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1
1
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1
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1
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650892
Shibata
Purification and characterizat ...
Scapharca broughtonii
Comp. Biochem. Physiol. B
134
307-314
2003
-
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9
2
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2
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2
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1
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2
2
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1
1
1
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1
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9
-
2
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2
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1
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2
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1
1
1
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1
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650894
Shibata
Nucleotides modulate the activ ...
Scapharca broughtonii
Comp. Biochem. Physiol. B
134
713-719
2003
4
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2
9
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2
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1
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2
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1
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10
-
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2
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4
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2
2
9
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1
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Okada
Distribution and purification ...
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2078
Soda
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PLP-dependent and independent ...
Enterococcus faecalis, Streptococcus thermophilus
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Yohda
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Adams
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Amino acid racemases and epime ...
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Lamont
Partial purification and chara ...
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