Information on EC 1.4.4.2 - glycine dehydrogenase (aminomethyl-transferring)

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

EC NUMBER
COMMENTARY hide
1.4.4.2
-
RECOMMENDED NAME
GeneOntology No.
glycine dehydrogenase (aminomethyl-transferring)
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
glycine + [glycine-cleavage complex H protein]-N6-lipoyl-L-lysine = [glycine-cleavage complex H protein]-S-aminomethyl-N6-dihydrolipoyl-L-lysine + CO2
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decarboxylation
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
glycine biosynthesis II
-
-
glycine cleavage
-
-
glycine metabolism
-
-
Glycine, serine and threonine metabolism
-
-
Metabolic pathways
-
-
NIL
-
-
SYSTEMATIC NAME
IUBMB Comments
glycine:H-protein-lipoyllysine oxidoreductase (decarboxylating, acceptor-amino-methylating)
A pyridoxal-phosphate protein. A component of the glycine cleavage system, which is composed of four components that only loosely associate: the P protein (EC 1.4.4.2), the T protein (EC 2.1.2.10, aminomethyltransferase), the L protein (EC 1.8.1.4, dihydrolipoyl dehydrogenase) and the lipoyl-bearing H protein [3]. Previously known as glycine synthase.
CAS REGISTRY NUMBER
COMMENTARY hide
37259-67-9
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
C3-plants
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
L. cv. Desiree
-
-
Manually annotated by BRENDA team
wheat
-
-
Manually annotated by BRENDA team
NADP-ME-type C4 plant from cultivar F7nxF2
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
glycine + His-tagged H-apoprotein
?
show the reaction diagram
-
very low activity
-
-
?
glycine + lipoate
?
show the reaction diagram
-
very low activity
-
-
?
glycine + lipoylated H-apoprotein
?
show the reaction diagram
-
very low activity
-
-
?
glycine + lipoylated His-tagged H-apoprotein
?
show the reaction diagram
-
very low activity
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
H1 protein
?
show the reaction diagram
-
substrate for L protein
-
-
?
H2 protein
?
show the reaction diagram
-
substrate for L protein
-
-
?
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5,5'-dithiobis-(2-nitrobenzoic acid)
complete inhibition
aminoacetonitrile
the inhibitor of GDC is able to mimic mitochondrial depolarization, hydrogen peroxide production, and cell death in response to stress or harpin treatment of cultured Arabidopsis cells
Aminooxyacetate
-
-
CO2
-
product inhibition
Co2+
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inhibition of glycine-CO2 exchange by binding of metal with H-protein-bound intermediate of glycine decarboxylation
Cu2+
-
inhibition of glycine-CO2 exchange by binding of metal with H-protein-bound intermediate of glycine decarboxylation
Fe2+
-
slight inhibition of glycine-CO2 exchange by binding of metal with H-protein-bound intermediate of glycine decarboxylation
Glycine methyl ester
-
-
harpin
the bacterial elicitor, a strong inducer of reactive oxygen species and NO, inhibits GDC activity
-
K2HPO4
-
inhibition of glycine-CO2 exchange reaction
KCl
-
inhibition of glycine-CO2 exchange reaction
Modified H-protein
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lipoic acid prosthetic group and cysteinyl residues modified with N-ethylmaleimide
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N-ethylmaleimide
N4-methylglutamine
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inhibition of glycine-CO2 exchange reaction
Ni2+
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inhibition of glycine-CO2 exchange by binding of metal with H-protein-bound intermediate of glycine decarboxylation
S-nitrosoglutathione
i.e. GSNO, the glycine decarboxylase complex, GDC activity is inhibited by S-nitrosoglutathione due to S-nitrosylation/S-glutathionylation of several cysteine residues, overview. The inhibition of GDC activity after GSNO treatment can be an indirect effect of ROS induced by inhibition of complex I
serine
C3-plants
-
competitive inhibitor
Zn2+
-
inhibition of glycine-CO2 exchange by binding of metal with H-protein-bound intermediate of glycine decarboxylation
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-mercaptoethanol
-
thiol compound required for maximal activity on glycine-CO2 exchange reaction
dithiothreitol
GSH
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thiol compound required for maximal activity on glycine-CO2 exchange reaction
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
31
bicarbonate
-
-
3.4
CO2
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glycine-CO2 exchange
0.0034 - 40
glycine
0.0026
H1 protein
-
L protein
-
0.0037
H2 protein
-
L protein
-
12.3
His-tagged H-apoprotein
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P-subunit, at pH 6
-
0.043
Lipoamide
-
the apparent Km-value of rTvL for binding the free lipoamide
0.47 - 12.3
lipoylated H-apoprotein
1 - 12.6
lipoylated His-tagged H-apoprotein
0.0046
pyridoxal phosphate
-
-
0.0026
rTvH1 protein
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the apparent Km-value of rTvL for binding rTvH1
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0.0037
rTvH2 protein
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the apparent Km-value of rTvL for binding rTvH2
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.602 - 6.08
Lipoamide
0.84
rTvH1 protein
Trichomonas vaginalis
-
kinetic parameter for L protein
-
2.08
rTvH2 protein
Trichomonas vaginalis
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kinetic parameter for L protein
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.02
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in 0.3 M mannitol, 10 mM KH2PO4, pH 7.2, with 5 mM MgCl2, 10 mM KCl, 0.1% (w/v) bovine serum albumin, 300 mM thiamine diphosphate, 200 mM NAD+, at 25C
additional information
-
mutations have a 6 to 8% of normal glycine decarboxylase activities when expressed in COS7 cells
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6
-
P-subunit
6.6
-
glycine-CO2 exchange
6.7
-
glycine-CO2 exchange
7
-
glycine-CO2 exchange
7.1
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glycine + lipoylprotein
7.4
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assay condition for determination of the interaction of recombinant H an L protein
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
-
assay at
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
highest expression
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
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protein P1/P2 complex is located predominantly in the cytoplasm
Manually annotated by BRENDA team
-
; H1, H2, and L protein. H and L proteins do not form a stable complex in the hydrogenosomes
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Synechocystis sp. (strain PCC 6803 / Kazusa)
Synechocystis sp. (strain PCC 6803 / Kazusa)
Synechocystis sp. (strain PCC 6803 / Kazusa)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
13900
-
predicted value TvH1 protein
14000
-
recombinant TvH1 protein, analysis of the native mass of TvH1 protein by gel filtration, SDS-PAGE and Western blot
14800
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predicted value TvH2 protein
15000
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recombinant TvH2 protein, analysis of the native mass of TvH2 protein by gel filtration, SDS-PAGE and Western blot
51800
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predicted value TvL protein
52000
-
recombinant TvL protein, analysis of the native mass of TvL protein by gel filtration, SDS-PAGE and Western blot
105000
-
predicted from amino acids
114400
-
calculation from cDNA
152000
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gel filtration
200000
208000
-
sucrose density gradient centrifugation
210000
220000
-
SDS-PAGE
225000
-
gel filtration
270000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
heterotetramer
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1 * 105000 + 1 * 60000 + 1 * 41000 + 1 * 14000, SDS-PAGE
homodimer
monomer
-
1 * 14000, SDS-PAGE, H1 protein, 1 * 15000, SDS-PAGE, H2 protein
tetramer
additional information
peptide mapping using trypsin degestion, overview
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
proteolytic modification
C3-plants
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-
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified recombinant His-tagged enzyme, hanging drop vapour diffusion, 18C, 0.004 ml of 40/mg/ml protein in 20 mM Tris-HCl, pH 7.8, 50 mM sodium chloride, and 10 mM 2-mercaptoethanol, are mixed with 0.004 ml of reservoir solution containing 100 mM Tris-HCl pH 7.75, 15-25% PEG 3350, 0.15-0.3 M CsCl or LiCl and 10 mM 2-mercaptoethanol, equilibration over 1 ml reservoir solution, method optimization, 1-3 days, streak-seeding at 20C, X-ray diffraction structure determination and analysis at 2.1 A resolution
hanging-drop vapour-difffusion method, crystals belong to the trigonal space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 89.5, c = 371.0 A
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vapour diffusion method with 30% w/v polyethylene glycol 3350 and 100 mM KSCN as the precipitant. Crystal structure of three forms of P-protein: the apoenzyme at 2.4 A resolution, the holoenzyme at 2.1 A resolution and the holoenzyme in complex with a substrate analog inhibitor (aminooxy)acetate
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 8
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P-subunit shows 50% lower activity at pH 8 than at pH 6
686720
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
70
-
1 min, complete loss of activity
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, several weeks
-
0-20C, 24 h, P-protein in purified P,L-protein fraction, 50-60% loss of activity
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
H1, H2, and L protein purified to homogeneity, more than 95% pure; using a nickel-nitrilotriacetic acid-agarose column
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Ni-NTA column chromatography
Q-Sepharose column chromatography and Sephacryl S-100 gel filtration
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recombinant His-tagged enzyme from Escherichia coli by nickel affinity and ion exchange chromatography, and gel filtration
ultracentrifugation
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Arabidopsis thaliana and Moricandia arvensis using Agrobacterium tumefaciens strain GV3101
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expressed in Escherichia coli BL21(DE3) cells
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expressed in Escherichia coli strains BL21 Gold and LMG194
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expressed in Flaveria bidentis (C4) and Arabidopsis thaliana (C3)
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expressed in Pichia pastoris strain GS115
expression of P-protein in yeast strains DS2-73U and DS2-75U
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expression of the His-tagged enzyme in Escherichia coli
into pGEM-T vector for DNA manipulations and sequence analysis using the Escherichia coli strain TG1
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into the pET-29B vector for expression in Escherichia coli BL21DE3 cells, into master-neo(HA)2 plasmid for transfection of Trichomonas vaginalis; pET-H1, pET-H2, and pET-L plasmids expressed in Escherichia coli BL21(DE3) cells
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missense mutations expressed in COS7 cells; two identified mutations, A389V and R739V, are introduced into the pEUK-(N) expression vector pEUK-(C1) carrying human glycine decarboxylase complementary DNA for expression in COS7 cells
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A389V
-
missense mutation, 6-8% of normal GLDC activity when expressed in COS7 cells
R739H
-
missense mutation, 6-8% of normal GLDC activity when expressed in COS7 cells
Mu0171
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T protein mutant, from the gene sll0171, an internal 1 kb fragment is deleted and replaced by the aphll gene
Mu293
-
P protein mutant, from the gene slr0293, an internal 2.1 kb fragment is deleted and replaced by the aphll gene
Mu879
-
H protein mutant, from the gene slr0879, an internal 0.2 kb fragment is deleted and replaced by the aphll gene
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
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mutations of the glycine decarboxylase gene are found in patients with nonketotic hyperglycinemia, NKH
additional information
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