BRENDA - Enzyme Database
show all sequences of 5.4.3.8

Crystal structure of glutamate-1-semialdehyde-2,1-aminomutase from Arabidopsis thaliana

Song, Y.; Pu, H.; Jiang, T.; Zhang, L.; Ouyang, M.; Acta Crystallogr. Sect. F 72, 448-456 (2016)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
gene AtGSA1, recombinant expression of His6-tagged enzyme lacking the N-terminal plastid-targeting sequences in Escherichia coli strain BL21(DE3)
Arabidopsis thaliana
Crystallization (Commentary)
Crystallization
Organism
purified recombinant detagged enzyme, sitting drop vapour diffusion method, mixing of 0.001 ml of 8 mg/ml protein in 20 mM Tris-HCl, pH 7.5, and 200 mM NaCl, with 0.001 ml of reservoir solution containing 0.15 M potassium bromide, and 30% w/v PEG 2000 MME, and equilibration against 0.2 ml reservoir solution, X-ray diffraction structure determination and analysis at 1.25 A resolution
Arabidopsis thaliana
Localization
Localization
Commentary
Organism
GeneOntology No.
Textmining
chloroplast
the enzyme has an N-terminal plastid-targeting sequence
Arabidopsis thaliana
9507
-
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
L-glutamate 1-semialdehyde
Arabidopsis thaliana
-
5-aminolevulinate
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Arabidopsis thaliana
P42799
-
-
Purification (Commentary)
Commentary
Organism
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, removal of the His-tag through TEV protease, followed by gel filtration, and ultrafiltration
Arabidopsis thaliana
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
L-glutamate 1-semialdehyde
-
746660
Arabidopsis thaliana
5-aminolevulinate
-
-
-
?
additional information
enzyme GSAM catalyzes the transamination of GSA substrate to form 5-aminolevulinate by an unusual intramolecular exchange of amino and oxo groups via the intermediate 4,5-diaminovalerate (DAVA). The reaction starts with imine formation between pyridoxamine 5'-phosphate and the aldehyde of GSA. During the first half of the reaction pyridoxamine 5'-phosphate is converted to pyridoxal 5'-phosphate, while pyridoxamine 5'-phosphate is regenerated in the second half of the reaction upon 5-aminolevulinate formation
746660
Arabidopsis thaliana
?
-
-
-
-
Subunits
Subunits
Commentary
Organism
dimer
enzyme AtGSA1 forms an asymmetric dimer and displays asymmetry in cofactor binding as well as in the gating-loop orientation
Arabidopsis thaliana
More
the overall structure of AtGSA1 consists of three sequentially arranged domains: the N-terminal domain (Val1-Asp63, mature protein) comprises one alpha-helix and a three-stranded antiparallel beta-sheet, the pyridoxamine 5'-phosphate/pyridoxal 5'-phosphate-binding domain (Tyr64-Gly328), which is also the catalytic domain, contains a central seven-stranded beta-sheet with one antiparallel and six parallel beta-strands, and the C-terminal domain (Thr329-Ile434) is composed of a three-stranded antiparallel beta-sheet with four helices covering the outer surface. Asymmetry of AtGSA1 in the gating-loop conformation, overview
Arabidopsis thaliana
Cofactor
Cofactor
Commentary
Organism
Structure
additional information
during the first half of the reaction pyridoxamine 5'-phosphate is converted to pyridoxal 5'-phosphate, while pyridoxamine 5'-phosphate is regenerated in the second half of the reaction upon 5-aminolevulinate formation
Arabidopsis thaliana
pyridoxal 5'-phosphate
a pyridoxamine 5'-phosphate (PMP)/pyridoxal 5'-phosphate (PLP)-dependent enzyme, binding structure, overview
Arabidopsis thaliana
pyridoxamine 5'-phosphate
a pyridoxamine 5'-phosphate (PMP)/pyridoxal 5'-phosphate (PLP)-dependent enzyme, binding structure, overview
Arabidopsis thaliana
Cloned(Commentary) (protein specific)
Commentary
Organism
gene AtGSA1, recombinant expression of His6-tagged enzyme lacking the N-terminal plastid-targeting sequences in Escherichia coli strain BL21(DE3)
Arabidopsis thaliana
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
additional information
during the first half of the reaction pyridoxamine 5'-phosphate is converted to pyridoxal 5'-phosphate, while pyridoxamine 5'-phosphate is regenerated in the second half of the reaction upon 5-aminolevulinate formation
Arabidopsis thaliana
pyridoxal 5'-phosphate
a pyridoxamine 5'-phosphate (PMP)/pyridoxal 5'-phosphate (PLP)-dependent enzyme, binding structure, overview
Arabidopsis thaliana
pyridoxamine 5'-phosphate
a pyridoxamine 5'-phosphate (PMP)/pyridoxal 5'-phosphate (PLP)-dependent enzyme, binding structure, overview
Arabidopsis thaliana
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified recombinant detagged enzyme, sitting drop vapour diffusion method, mixing of 0.001 ml of 8 mg/ml protein in 20 mM Tris-HCl, pH 7.5, and 200 mM NaCl, with 0.001 ml of reservoir solution containing 0.15 M potassium bromide, and 30% w/v PEG 2000 MME, and equilibration against 0.2 ml reservoir solution, X-ray diffraction structure determination and analysis at 1.25 A resolution
Arabidopsis thaliana
Localization (protein specific)
Localization
Commentary
Organism
GeneOntology No.
Textmining
chloroplast
the enzyme has an N-terminal plastid-targeting sequence
Arabidopsis thaliana
9507
-
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
L-glutamate 1-semialdehyde
Arabidopsis thaliana
-
5-aminolevulinate
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, removal of the His-tag through TEV protease, followed by gel filtration, and ultrafiltration
Arabidopsis thaliana
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
L-glutamate 1-semialdehyde
-
746660
Arabidopsis thaliana
5-aminolevulinate
-
-
-
?
additional information
enzyme GSAM catalyzes the transamination of GSA substrate to form 5-aminolevulinate by an unusual intramolecular exchange of amino and oxo groups via the intermediate 4,5-diaminovalerate (DAVA). The reaction starts with imine formation between pyridoxamine 5'-phosphate and the aldehyde of GSA. During the first half of the reaction pyridoxamine 5'-phosphate is converted to pyridoxal 5'-phosphate, while pyridoxamine 5'-phosphate is regenerated in the second half of the reaction upon 5-aminolevulinate formation
746660
Arabidopsis thaliana
?
-
-
-
-
Subunits (protein specific)
Subunits
Commentary
Organism
dimer
enzyme AtGSA1 forms an asymmetric dimer and displays asymmetry in cofactor binding as well as in the gating-loop orientation
Arabidopsis thaliana
More
the overall structure of AtGSA1 consists of three sequentially arranged domains: the N-terminal domain (Val1-Asp63, mature protein) comprises one alpha-helix and a three-stranded antiparallel beta-sheet, the pyridoxamine 5'-phosphate/pyridoxal 5'-phosphate-binding domain (Tyr64-Gly328), which is also the catalytic domain, contains a central seven-stranded beta-sheet with one antiparallel and six parallel beta-strands, and the C-terminal domain (Thr329-Ile434) is composed of a three-stranded antiparallel beta-sheet with four helices covering the outer surface. Asymmetry of AtGSA1 in the gating-loop conformation, overview
Arabidopsis thaliana
General Information
General Information
Commentary
Organism
additional information
structure-function analysis., overview. Enzyme AtGSA1 forms an asymmetric dimer and displays asymmetry in cofactor binding as well as in the gating-loop orientation. The mobility of residues Gly163, Ser164 and Gly165 is important for reorientation of the gating loop. The asymmetry of the AtGSA1 structure supports the previously proposed negative cooperativity between monomers of GSAM
Arabidopsis thaliana
General Information (protein specific)
General Information
Commentary
Organism
additional information
structure-function analysis., overview. Enzyme AtGSA1 forms an asymmetric dimer and displays asymmetry in cofactor binding as well as in the gating-loop orientation. The mobility of residues Gly163, Ser164 and Gly165 is important for reorientation of the gating loop. The asymmetry of the AtGSA1 structure supports the previously proposed negative cooperativity between monomers of GSAM
Arabidopsis thaliana
Other publictions for EC 5.4.3.8
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)
747005
Li
Crystal structure of a glutam ...
Pseudomonas aeruginosa, Pseudomonas aeruginosa ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Biochem. Biophys. Res. Commun.
500
804-809
2018
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746660
Song
Crystal structure of glutamat ...
Arabidopsis thaliana
Acta Crystallogr. Sect. F
72
448-456
2016
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1
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747678
Ramzi
5-Aminolevulinic acid product ...
Corynebacterium glutamicum, Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Enzyme Microb. Technol.
81
1-7
2015
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727125
Campanini
Asymmetry of the active site l ...
Synechococcus sp.
BioMed Res. Int.
2013
353270
2013
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1
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716103
Kang
Engineering Escherichia coli f ...
Escherichia coli, Escherichia coli MG1655
Metab. Eng.
13
492-498
2011
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1
1
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703619
Orriss
Absence of a catalytic water c ...
Synechococcus sp.
FASEB J.
24
404-414
2010
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714041
Ge
Crystal structure of glutamate ...
Bacillus subtilis
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356-360
2010
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677347
Lv
Cloning, expression, purificat ...
Bacillus subtilis
Acta Crystallogr. Sect. F
62
483-485
2006
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1
1
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4
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682509
Stetefeld
Intersubunit signaling in glut ...
Synechococcus sp.
Proc. Natl. Acad. Sci. USA
103
13688-13693
2006
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662360
Lüer
Complex formation between glut ...
Escherichia coli
J. Biol. Chem.
280
18568-18572
2005
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653764
Tsang
Expression of a Brassic napus ...
Brassica napus
Protein Expr. Purif.
29
193-201
2003
1
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649844
Smith
Transient-state kinetic analys ...
Synechococcus sp.
Biochemistry
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1998
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3445
Grimm
-
Crystal structure of glutamate ...
Synechococcus sp.
Proc. Natl. Acad. Sci. USA
84
4866-4871
1997
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3440
Palmieri
Glutamate-1-semialdehyde amino ...
Saccharolobus solfataricus, Saccharolobus solfataricus P2
Biochem. J.
320
541-545
1996
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3435
Brody
Characterization of the differ ...
Synechococcus sp.
Biochemistry
34
15918-15924
1995
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3421
Henning
Crystallization and preliminar ...
Synechococcus sp.
J. Mol. Biol.
242
591-594
1994
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3434
Mayer
Metal requirement of the enzym ...
Chlorella vulgaris, Synechococcus sp.
Arch. Biochem. Biophys.
312
203-209
1994
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721440
Matters
-
Biosynthesis of delta-aminolev ...
Saccharolobus solfataricus, Saccharolobus solfataricus 98-3
Arch. Microbiol.
161
272-276
1994
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3442
Tyacke
Properties of the pyridoxaldim ...
Pisum sativum
Biochem. J.
293
697-791
1993
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2
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3443
Murakami
Cloning and characterization o ...
Propionibacterium freudenreichii
Appl. Environ. Microbiol.
59
347-350
1993
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1
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1
1
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-
3444
Murakami
Cloning and characterization o ...
Xanthomonas campestris
Appl. Microbiol. Biotechnol.
38
502-506
1993
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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
1
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1
1
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3427
Berry-Lowe
Purification and characterizat ...
Hordeum vulgare
Plant Physiol.
99
1597-1603
1992
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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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1
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3
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1
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1
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1
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1
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3
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1
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3430
Smith
Gabaculine resistance of Synec ...
Synechococcus sp.
Biochemistry
31
4122-4127
1992
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1
-
1
-
1
2
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3
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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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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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1
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2
-
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3432
Ilag
Activity and spectroscopic pro ...
Escherichia coli
Biochemistry
31
7143-7151
1992
2
-
1
-
1
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-
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1
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2
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4
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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4
1
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3433
Smith
Glutamate 1-semialdehyde amino ...
Synechococcus sp.
Biochemistry
31
11249-11254
1992
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1
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1
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-
1
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3439
Pugh
Mechanism of glutamate semiald ...
Pisum sativum
J. Biol. Chem.
267
1584-1588
1992
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1
1
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1
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3
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1
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1
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1
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1
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3
-
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-
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3426
Rieble
Separation and partial charact ...
Synechococcus sp.
Arch. Biochem. Biophys.
289
289-297
1991
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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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1
1
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1
-
2
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3436
Jahn
Purification and functional ch ...
Chlamydomonas reinhardtii
J. Biol. Chem.
266
161-167
1991
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2
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1
1
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3
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1
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1
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2
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
1
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1
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1
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2
1
-
-
-
-
1
1
-
-
-
-
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-
-
3438
Nair
Direct identification and quan ...
Pisum sativum
FEBS Lett.
283
4-6
1991
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2
1
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1
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1
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1
1
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2
1
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1
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-
1
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-
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2
1
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-
1
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1
1
-
2
1
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-
-
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-
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3441
Smith
Characterization of glutamate- ...
Synechococcus sp.
Eur. J. Biochem.
202
749-757
1991
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1
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3
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1
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3
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1
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-
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1
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1
1
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-
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1
-
3
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3
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-
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1
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3429
Bull
-
Cyanobacterial glutamate 1-sem ...
Synechococcus sp.
Arch. Microbiol.
154
56-59
1990
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3
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1
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1
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1
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3
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1
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3431
Nair
Inhibition studies on 5-amino- ...
Pisum sativum
Biochem. Soc. Trans.
18
656-657
1990
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2
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1
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2
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1
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1
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2
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3437
Grimm
Primary structure of a key enz ...
Hordeum vulgare
Proc. Natl. Acad. Sci. USA
87
4169-4173
1990
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4
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2
1
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1
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-
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2
1
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2
1
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3428
Grimm
Purification and partial amino ...
Hordeum vulgare, Synechococcus sp.
Carlsberg Res. Commun.
54
67-79
1989
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2
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6
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2
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2
2
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2
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2
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2
2
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3424
Mau
Biosynthesis of delta-aminolev ...
Chlamydomonas reinhardtii
Plant Physiol.
86
793-797
1988
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1
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1
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1
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3425
Hoober
Biosynthesis of DELTA-aminolev ...
Hordeum vulgare
Carlsberg Res. Commun.
53
11-25
1988
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1
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1
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-
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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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-
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3423
Kannangara
-
Biosynthesis of DELTA-aminolev ...
Hordeum vulgare
Carlsberg Res. Commun.
50
179-191
1985
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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
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1
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1
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1
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2
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-
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3422
Wang
Purification, characterization ...
Chlamydomonas reinhardtii
Plant Physiol.
74
569-575
1984
-
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-
-
-
-
-
-
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1
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3
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-
-
1
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-
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-
-
-
-
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-
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1
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-
-
-
1
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-
-
-
-
-
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-
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3420
Kannangara
-
Biosynthesis of DELTA-aminolev ...
Hordeum vulgare
Carlsberg Res. Commun.
44
11-20
1979
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-
-
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1
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1
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1
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-
1
-
-
2
-
-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
-
1
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-
1
-
-
-
-
-
1
-
-
2
-
-
-
-
-
-
-
-
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-
-
-
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-
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3419
Kannangara
-
Biosynthesis of DELTA-aminolev ...
Hordeum vulgare
Carlsberg Res. Commun.
43
185-194
1978
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-
-
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7
1
2
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2
1
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1
-
-
1
-
-
1
-
-
2
1
1
1
-
-
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
7
-
1
2
-
2
1
-
-
-
1
-
1
-
-
2
1
1
1
-
-
1
1
-
-
-
-
-
-
-
-