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show all sequences of 1.4.4.2

Glycine decarboxylase is an unusual amino acid decarboxylase involved in tumorigenesis

Go, M.K.; Zhang, W.C.; Lim, B.; Yew, W.S.; Biochemistry 53, 947-956 (2014)

Data extracted from this reference:

Activating Compound
Activating Compound
Commentary
Organism
Structure
H-protein
upon addition of exogenous unlipoylated H-protein, kcat increases 190fold, in the absence of the lipoic acid moiety on H-protein, the methylamine adduct with pyridoxal 5'-phosphate (aminomethyl-quinonoid intermediate) is released as the product of the GLDC-catalyzed decarboxylation of glycine
Homo sapiens
lipoylated H-protein
the presence of the lipoyl moiety on H-protein does not affect the rates of GLDC (or GLDCcoexp)-catalyzed glycine decarboxylation
Homo sapiens
additional information
the presence of the lipoyl moiety on H-protein does not affect the rates of GLDC (or GLDCcoexp)-catalyzed glycine decarboxylation further corroborates the suggestion that H-protein (or lipoylated H-protein) does not directly participate in and is not required for release of CO2 from glycine in the formation of the pyridoxal 5'-phosphate-quinonoid intermediate, an important distinction that is contrary to earlier findings
Homo sapiens
Cloned(Commentary)
Commentary
Organism
recombinant expression of codon optimized C-terminally His6-tagged enzyme GLDC in Escherichia coli strain BL21(DE3), GLDC is expressed either separately (without H-protein) or simultaneously with H-protein, coexpression of His6-tagged enzyme with codon-optimized human H-protein in Escherichia coli strain BL21(DE3) from pJexpress-416 vector
Homo sapiens
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.0003
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme
Homo sapiens
0.00031
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of lipoylated H-protein
Homo sapiens
0.00037
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of H-protein
Homo sapiens
1.3
-
glycine
pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of lipoylated H-protein
Homo sapiens
2.1
-
glycine
pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of H-protein
Homo sapiens
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Mg2+
required
Homo sapiens
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
glycine + [glycine-cleavage complex H protein]-N6-lipoyl-L-lysine
Homo sapiens
-
[glycine-cleavage complex H protein]-S-aminomethyl-N6-dihydrolipoyl-L-lysine + CO2
-
-
r
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Homo sapiens
P23378
-
-
Purification (Commentary)
Commentary
Organism
recombinant His6-tagged enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and dialysis
Homo sapiens
Reaction
Reaction
Commentary
Organism
glycine + [glycine-cleavage complex H protein]-N6-lipoyl-L-lysine = [glycine-cleavage complex H protein]-S-aminomethyl-N6-dihydrolipoyl-L-lysine + CO2
mechanism of the GLDC-catalyzed reaction, detailed overview. GLDC is an unusual PLP-containing alpha-amino acid decarboxylase that removes carbon dioxide from the glycine substrate without releasing the expected amine (methylamine, a metabolic precursor of toxic formaldehyde) as a product. In an unusual decarboxylation mechanism, the resulting aminomethyl moiety is instead transferred to an accessory H-protein. (1) H-Protein is not required for glycine decarboxylation but, instead, is required for the release of the aminomethyl moiety from the quinonoid adduct. (2) Glycine decarboxylation is reversible and presumably proceeds through a stable quinonoid intermediate. (3) The physiological product of glycine decarboxylation is H-protein-S-aminomethyl dihydrolipoyllysine and not methylamine (in the absence of H-protein, the aminomethyl moiety remains as a quinonoid adduct)
Homo sapiens
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
glycine + [glycine-cleavage complex H protein]-N6-lipoyl-L-lysine
-
741906
Homo sapiens
[glycine-cleavage complex H protein]-S-aminomethyl-N6-dihydrolipoyl-L-lysine + CO2
-
-
-
r
glycine + [glycine-cleavage complex H protein]-N6-lipoyl-L-lysine
reversible reaction
741906
Homo sapiens
[glycine-cleavage complex H protein]-S-aminomethyl-N6-dihydrolipoyl-L-lysine + CO2
-
-
-
r
additional information
presence of excess pyridoxal 5'-phosphate is used in the assay mixture to facilitate the displacement of the quinonoid intermediate in the absence of an acceptor for the methylamine moiety (of decarboxylated glycine) to allow multiple enzyme turnovers. Mass spectrometry and 13C NMR spectroscopy are used to determine the products of glycine decarboxylation. The assay reaction mixtures are incubated for 1 week at pH 7.0, 25°C
741906
Homo sapiens
?
-
-
-
-
Subunits
Subunits
Commentary
Organism
monomer
1 * 112730, mass spectrometry
Homo sapiens
More
recombinant human GLDC is active in the monomeric form, unlike GLDC orthologues in chicken and Synechocystis where the enzyme exists as a homodimer
Homo sapiens
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
25
-
assay at
Homo sapiens
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.0001
-
glycine
pH 7.0, 25°C, recombinant individually expressed wild-type enzyme
Homo sapiens
0.00014
-
glycine
pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of lipoic acid
Homo sapiens
0.016
-
glycine
pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of lipoylated H-protein
Homo sapiens
0.019
-
glycine
pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of H-protein
Homo sapiens
0.031
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme
Homo sapiens
0.033
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of H-protein
Homo sapiens
0.047
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of lipoylated H-protein
Homo sapiens
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
-
assay at
Homo sapiens
Cofactor
Cofactor
Commentary
Organism
Structure
pyridoxal 5'-phosphate
-
Homo sapiens
Activating Compound (protein specific)
Activating Compound
Commentary
Organism
Structure
H-protein
upon addition of exogenous unlipoylated H-protein, kcat increases 190fold, in the absence of the lipoic acid moiety on H-protein, the methylamine adduct with pyridoxal 5'-phosphate (aminomethyl-quinonoid intermediate) is released as the product of the GLDC-catalyzed decarboxylation of glycine
Homo sapiens
lipoylated H-protein
the presence of the lipoyl moiety on H-protein does not affect the rates of GLDC (or GLDCcoexp)-catalyzed glycine decarboxylation
Homo sapiens
additional information
the presence of the lipoyl moiety on H-protein does not affect the rates of GLDC (or GLDCcoexp)-catalyzed glycine decarboxylation further corroborates the suggestion that H-protein (or lipoylated H-protein) does not directly participate in and is not required for release of CO2 from glycine in the formation of the pyridoxal 5'-phosphate-quinonoid intermediate, an important distinction that is contrary to earlier findings
Homo sapiens
Cloned(Commentary) (protein specific)
Commentary
Organism
recombinant expression of codon optimized C-terminally His6-tagged enzyme GLDC in Escherichia coli strain BL21(DE3), GLDC is expressed either separately (without H-protein) or simultaneously with H-protein, coexpression of His6-tagged enzyme with codon-optimized human H-protein in Escherichia coli strain BL21(DE3) from pJexpress-416 vector
Homo sapiens
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
pyridoxal 5'-phosphate
-
Homo sapiens
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.0003
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme
Homo sapiens
0.00031
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of lipoylated H-protein
Homo sapiens
0.00037
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of H-protein
Homo sapiens
1.3
-
glycine
pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of lipoylated H-protein
Homo sapiens
2.1
-
glycine
pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of H-protein
Homo sapiens
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Mg2+
required
Homo sapiens
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
glycine + [glycine-cleavage complex H protein]-N6-lipoyl-L-lysine
Homo sapiens
-
[glycine-cleavage complex H protein]-S-aminomethyl-N6-dihydrolipoyl-L-lysine + CO2
-
-
r
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant His6-tagged enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and dialysis
Homo sapiens
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
glycine + [glycine-cleavage complex H protein]-N6-lipoyl-L-lysine
-
741906
Homo sapiens
[glycine-cleavage complex H protein]-S-aminomethyl-N6-dihydrolipoyl-L-lysine + CO2
-
-
-
r
glycine + [glycine-cleavage complex H protein]-N6-lipoyl-L-lysine
reversible reaction
741906
Homo sapiens
[glycine-cleavage complex H protein]-S-aminomethyl-N6-dihydrolipoyl-L-lysine + CO2
-
-
-
r
additional information
presence of excess pyridoxal 5'-phosphate is used in the assay mixture to facilitate the displacement of the quinonoid intermediate in the absence of an acceptor for the methylamine moiety (of decarboxylated glycine) to allow multiple enzyme turnovers. Mass spectrometry and 13C NMR spectroscopy are used to determine the products of glycine decarboxylation. The assay reaction mixtures are incubated for 1 week at pH 7.0, 25°C
741906
Homo sapiens
?
-
-
-
-
Subunits (protein specific)
Subunits
Commentary
Organism
monomer
1 * 112730, mass spectrometry
Homo sapiens
More
recombinant human GLDC is active in the monomeric form, unlike GLDC orthologues in chicken and Synechocystis where the enzyme exists as a homodimer
Homo sapiens
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
25
-
assay at
Homo sapiens
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.0001
-
glycine
pH 7.0, 25°C, recombinant individually expressed wild-type enzyme
Homo sapiens
0.00014
-
glycine
pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of lipoic acid
Homo sapiens
0.016
-
glycine
pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of lipoylated H-protein
Homo sapiens
0.019
-
glycine
pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of H-protein
Homo sapiens
0.031
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme
Homo sapiens
0.033
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of H-protein
Homo sapiens
0.047
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of lipoylated H-protein
Homo sapiens
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
-
assay at
Homo sapiens
General Information
General Information
Commentary
Organism
physiological function
glycine decarboxylase is an unusual amino acid decarboxylase involved in tumorigenesis. In humans, GLDC is part of a multienzyme complex (which includes the lipoyl-containing H-protein) that couples the decarboxylation of glycine to the biosynthesis of serine
Homo sapiens
General Information (protein specific)
General Information
Commentary
Organism
physiological function
glycine decarboxylase is an unusual amino acid decarboxylase involved in tumorigenesis. In humans, GLDC is part of a multienzyme complex (which includes the lipoyl-containing H-protein) that couples the decarboxylation of glycine to the biosynthesis of serine
Homo sapiens
KCat/KM [mM/s]
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.009
-
glycine
pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of H-protein
Homo sapiens
0.012
-
glycine
pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of lipoylated H-protein
Homo sapiens
100
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme
Homo sapiens
150
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of lipoylated H-protein
Homo sapiens
890
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of H-protein
Homo sapiens
KCat/KM [mM/s] (protein specific)
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.009
-
glycine
pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of H-protein
Homo sapiens
0.012
-
glycine
pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of lipoylated H-protein
Homo sapiens
100
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme
Homo sapiens
150
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of lipoylated H-protein
Homo sapiens
890
-
glycine
pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of H-protein
Homo sapiens
Other publictions for EC 1.4.4.2
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)
741906
Go
Glycine decarboxylase is an u ...
Homo sapiens
Biochemistry
53
947-956
2014
3
-
1
-
-
-
-
5
-
1
-
1
-
2
-
-
1
1
-
-
-
-
3
2
1
-
-
7
1
-
-
1
-
-
-
3
-
1
1
-
-
-
-
-
-
5
-
1
-
1
-
-
-
1
-
-
-
-
3
2
1
-
-
7
1
-
-
-
-
1
1
-
5
5
743023
Azize
Mutation analysis of glycine ...
Homo sapiens
J. Hum. Genet.
59
593-597
2014
-
-
1
-
1
-
-
-
-
-
-
-
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
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-
-
-
-
-
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1
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1
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-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
743266
Varadarajan
Plasmodium berghei glycine cl ...
no activity in Plasmodium berghei
Mol. Biochem. Parasitol.
197
50-55
2014
-
-
-
-
-
-
-
-
-
-
-
-
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3
-
-
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-
-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
724693
Dominy
Glycine decarboxylase cleaves ...
Mus musculus
Cancer Cell
21
143-145
2012
-
-
-
-
-
-
-
-
-
-
-
1
-
1
-
-
-
-
-
2
-
-
1
-
-
-
-
-
-
-
-
-
-
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-
-
-
-
-
-
-
-
-
-
-
-
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1
-
-
-
-
-
2
-
-
1
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
725016
Timm
Glycine decarboxylase controls ...
Arabidopsis thaliana
FEBS Lett.
586
3692-3697
2012
-
-
-
-
-
-
-
-
1
-
-
1
-
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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1
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-
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-
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1
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
724197
Zay
Glycine cleavage enzyme comple ...
Homo sapiens
Biochem. Cell Biol.
89
299-307
2011
-
-
1
-
-
-
-
-
-
-
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1
-
5
-
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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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1
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2
-
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1
-
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-
-
-
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-
-
1
1
-
-
-
725115
Zhang
-
Transcriptionally and phylogen ...
Brassica napus
Hortic. Environ. Biotechnol.
52
427-434
2011
-
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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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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
710748
Hasse
Crystallization and preliminar ...
Synechocystis sp.
Acta Crystallogr. Sect. F
66
187-191
2010
-
-
1
1
-
-
-
-
-
-
1
1
-
4
-
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1
-
-
-
-
-
2
1
-
-
-
-
-
-
-
1
-
-
-
-
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1
1
1
-
-
-
-
-
-
-
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1
1
-
-
-
1
-
-
-
-
2
1
-
-
-
-
-
-
-
-
-
2
2
-
-
-
713311
Palmieri
Regulation of plant glycine de ...
Arabidopsis thaliana
Plant Physiol.
152
1514-1528
2010
-
-
-
-
-
-
5
-
1
-
-
-
-
3
-
-
-
-
-
1
-
-
-
1
-
-
-
-
-
-
-
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-
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-
-
-
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-
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5
-
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1
-
-
-
-
-
-
-
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1
-
-
-
1
-
-
-
-
-
-
-
-
-
3
3
-
-
-
719865
Okamura-Ikeda
Crystal structure of aminometh ...
Escherichia coli
J. Biol. Chem.
285
18684-18692
2010
-
-
-
-
-
-
-
-
-
-
-
1
-
4
-
-
-
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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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-
-
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1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
697916
Hasse
Alternative splicing produces ...
Flaveria trinervia
FEBS J.
276
6985-6991
2009
-
-
1
-
-
-
-
-
1
-
-
-
-
6
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