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
1.4.4.2
-
RECOMMENDED NAME
GeneOntology No.
glycine dehydrogenase (aminomethyl-transferring)
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
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
H-protein ping-pong mechanism
-
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
mechanism
-
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
mechanism; sequential random bi bi mechanism in which no abortive dead end complex is formed
-
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 ACCESSION NO.
COMMENTARY
LITERATURE
decarboxylation
-
-
-
-
decarboxylation
-
-
decarboxylation
-
-
decarboxylation
-
co-substrate is H-protein, a lipoid acid-containing protein
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
glycine biosynthesis II
-
glycine cleavage
-
Glycine, serine and threonine metabolism
-
Metabolic pathways
-
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.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
decarboxylase, glycine
-
-
-
-
GDC
-
a four-protein system comprising three enzymes (P-protein, T-protein, and L-protein) plus H-protein
GDC
P15505
-
GDC
P23434
-
GDC
A9PL02
GDC is composed of four subunits, designated P-, H-, T-, and L-proteins, encoded by nuclear genes with N-terminal mitochondrial targeting pre-sequences, the Populus genome contains eight transcriptionally active GDC genes, encoding four H-proteins, two T-proteins, and single P- and L-proteins
GDC
-
-
GLDC
-
-
GLDP
-
serves as the actual decarboxylating unit of GDC
Gly decarboxylase complex
-
-
Gly decarboxylase H1
P25855
-
glycine cleavage enzyme complex
P23434
-
glycine cleavage H protein
-
-
glycine cleavage system H protein 1
P25855
-
Glycine cleavage system P-protein
-
-
-
-
glycine decarboxylase
-
-
-
-
glycine decarboxylase
-
-
glycine decarboxylase
-
-
glycine decarboxylase
-
-
glycine decarboxylase
-
-
glycine decarboxylase
-
-
glycine decarboxylase (P-protein)
-
-
glycine decarboxylase complex
P25855
-
glycine decarboxylase complex
A9PL02
the glycine decarboxylase complex cooperates with serine hydroxymethyltransferase to mediate photorespiratory glycine-serine interconversion
glycine decarboxylase complex
-
-
glycine decarboxylase complex
-
-
glycine decarboxylase complex
-
-
glycine decarboxylase complex
-
-
glycine decarboxylase complex H
P25855
-
glycine decarboxylase P-protein
-
-
-
-
glycine dehydrogenase
-
-
glycine dehydrogenase
-
-
glycine dehydrogenase
-
-
glycine dehydrogenase
-
-
glycine dehydrogenase
-
-
glycine dehydrogenase (decarboxylating)
-
-
-
-
glycine-cleavage complex
-
-
-
-
H protein
-
-
H-protein
P23434
-
H1 protein
-
-
H2 protein
-
-
P protein
-
-
P protein
-
-
P-protein
-
-
-
-
P-protein
P25855
-
P-protein
-
part of the glycine cleavage system
P-protein
-
-
P-protein
-
-
P-protein
A9PL02
-
P-protein
-
-
P-protein
-
-
P-protein (glycine decarboxylase)
-
-
P-subunit
-
serves as the actual decarboxylating unit of GDC
Protein P1
-
-
-
-
additional information
-
glycine decarboxylase, or P-protein, is part of the glycine cleavage system, GCS
CAS REGISTRY NUMBER
COMMENTARY
37259-67-9
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
ecotype Col-0
-
-
Manually annotated by BRENDA team
C3-plants
-
-
-
Manually annotated by BRENDA team
; adult patients with mild hyperglycinemia, infantile hypotonia, mental retardation, behavioral hyperirritability, and aggressive outbursts
-
-
Manually annotated by BRENDA team
L. cv. Desiree
-
-
Manually annotated by BRENDA team
strain PCC 6803
-
-
Manually annotated by BRENDA team
NADP-ME-type C4 plant from cultivar F7nxF2
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
metabolism
P74416
glycine decarboxylase is a major enzyme that is involved in the C1 metabolism of all organisms and in the photorespiratory pathway of plants and cyanobacteria. GCS is also essential in the plant photorespiratory C2 cycle, which salvages 2-phosphoglycolate resulting from the oxygenation reaction catalysed by ribulose-1,5-bisphosphate carboxylase/oxygenase under atmospheric conditions. The complete GCS reaction cycle requires the cooperation of three different enzymes, P-protein, T-protein and L-protein, and the small heat-stable H-protein, pathway overview
physiological function
P25855
role of GDC in the harpin-induced plant defense response, overview
physiological function
P23434
the H-protein interacts with the L-protein, which is also part of the L-ketoglutarate dehydrogenase complex
physiological function
-
enzyme overexpression promotes glycolysis, serine/glycine metabolism, and the accumulation of pyrimidine nucleotides. Enzyme overexpression alone is able to transform NIH 3T3 cells in vitro and drive tumor formation in vivo
physiological function
-
overexpression of the H-protein of glycine decarboxylase considerably enhances net-photosynthesis and growth of Arabidopsis thaliana. Glycine decarboxylase is an important feed-back signaller that contributes to the control of the Calvin-Benson cycle and hence carbon flow through both photosynthesis and photorespiration
metabolism
P25855
the glycine decarboxylase complex, GDC, is a key enzyme of the photorespiratory C2 cycle in C3 plants, regulation of plant glycine decarboxylase by S-nitrosylation and glutathionylation, overview. GDC activity is inhibited by S-nitrosoglutathione due to S-nitrosylation/S-glutathionylation of several cysteine residues
additional information
P74416
glycine decarboxylase, or P-protein, is part of the glycine cleavage system, GCS
additional information
P25855
the mitochondrial photorespiratory system is involved in the regulation of NO signal transduction in Arabidopsis thaliana
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
-
-
-
-
?
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
-
-
-
-
?
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
-
-
-
-
?
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
-
-
-
-
?
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
-
-
-
-
?
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
P74416, -
-
-
-
?
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
-
-
-
-
?
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
-, P23434
-
-
-
?
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
P74416, -
P-protein is the actual glycine-decarboxylating enzyme and uses pyridoxal 5'-phosphate as a cofactor. CO2 is released in the reaction and the residual aminomethyl group is bound to the oxidized lipoamide arm of H-protein
the methylene group is accepted by tetrahydrofolate to yield methylene tetrahydrofolate, a major cofactor in one-carbon metabolism
-
?
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
-
-
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
-
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
-
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
-
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
C3-plants
-
-
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
P15505
-
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
reaction is stimulated by lipoic acid which is a functional group of the H-protein
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
glycine decarboxylation catalyzed by P-protein alone is extremely low, lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
H1 protein
?
show the reaction diagram
-
substrate for L protein
-
-
?
H2 protein
?
show the reaction diagram
-
substrate for L protein
-
-
?
additional information
?
-
-
-
-
-
-
additional information
?
-
-
P-protein also catalyzes exchange of carbonyl carbon of glycine with CO2, reaction greatly stimulated by addition of H protein
-
-
-
additional information
?
-
-
P-protein also catalyzes exchange of carbonyl carbon of glycine with CO2, reaction greatly stimulated by addition of H protein
-
-
-
additional information
?
-
-
the enzyme is a component of the reversible glycine cleavage system, previously known as glycine synthase
-
-
-
additional information
?
-
-
glycine decarboxylase does not occur as a complex of all four proteins, but L-protein takes part in both glycine decarboxylase as well as in glycine reductase reaction
-
-
-
additional information
?
-
-
the glycine cleavage system consists of 4 protein components: 1. P-protein is a pyridoxal containing protein: a Schiff base is formed between the hydroxyl group of the pyridoxal phosphate and the alpha-NH2 of glycine, the amino group and the alpha-carbon of the glycine are transferred to the lipoamide cofactor of the second enzyme of the complex the H-protein, the alpha-carbonyl group of glycine is lost as CO2, 2. H-protein, 3. T-protein: catalyzes the passage of alpha-carbon from lipoamide of H protein to tetrahydrofolate, alpha-NH2 from glycine is lost as NH4+, 4. L-protein: catalyzes oxidation of reduced lipoamide back to its original form with concomitant reduction of NAD+ to NADH
-
-
-
additional information
?
-
-
nonketotic hyperglycinaemia is an autosomal recessive disorder of glycine metabolism caused by a deficiency in the mitochondrial glycine cleavage enzyme. The majority of cases are caused by mutations in the P-protein
-
-
-
additional information
?
-
-
in transgenic potato plants with an antisense reduction in P-protein of GDC, the decrease in photorespiratory decarboxylation is compensated for by an increase in respiratory decarboxylation in the light
-
-
-
additional information
?
-
-
the GDC H-protein (GLDH) has no catalytic activity itself but interacts via its lipoyl arm one after the other with the three other GDC subunits, P-protein (EC 1.4.4.2), T-protein (EC 2.1.2.10), and L-protein (EC 1.8.1.4), the GDC H-protein is a substrate for P-protein of glycine decarboxylase
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
-
-
-
-
?
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
-
-
-
-
?
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
-
-
-
-
?
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
-
-
-
-
?
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
-
-
-
-
?
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
-
-
-
-
?
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
-, P23434
-
-
-
?
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
show the reaction diagram
P74416, -
P-protein is the actual glycine-decarboxylating enzyme and uses pyridoxal 5'-phosphate as a cofactor. CO2 is released in the reaction and the residual aminomethyl group is bound to the oxidized lipoamide arm of H-protein
the methylene group is accepted by tetrahydrofolate to yield methylene tetrahydrofolate, a major cofactor in one-carbon metabolism
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
-
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
-
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
C3-plants
-
-
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
P15505
-
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
reaction is stimulated by lipoic acid which is a functional group of the H-protein
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
glycine decarboxylation catalyzed by P-protein alone is extremely low, lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
glycine + lipoylprotein
S-aminomethyldihydrolipoylprotein + CO2
show the reaction diagram
-
lipoyl protein: H-protein, lipoamide can also act as acceptor
-
-
?
additional information
?
-
-
nonketotic hyperglycinaemia is an autosomal recessive disorder of glycine metabolism caused by a deficiency in the mitochondrial glycine cleavage enzyme. The majority of cases are caused by mutations in the P-protein
-
-
-
additional information
?
-
-
in transgenic potato plants with an antisense reduction in P-protein of GDC, the decrease in photorespiratory decarboxylation is compensated for by an increase in respiratory decarboxylation in the light
-
-
-
COFACTOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
pyridoxal 5'-phosphate
-
bound
pyridoxal 5'-phosphate
-
-
pyridoxal 5'-phosphate
-
loosly bound
pyridoxal 5'-phosphate
-
pyridoxal phosphate binding site
pyridoxal 5'-phosphate
-
-
pyridoxal 5'-phosphate
-
2 mol of pyridoxal phosphate bound per mol of enzyme
pyridoxal 5'-phosphate
-
-
pyridoxal 5'-phosphate
C3-plants
-
-
pyridoxal 5'-phosphate
-
binding to the apoenzyme induces large open-closed conformational changes, with residues moving up to 13.5 A
pyridoxal 5'-phosphate
-
-
pyridoxal 5'-phosphate
P15505
-
pyridoxal 5'-phosphate
P74416
P-protein is the actual glycine-decarboxylating enzyme and uses pyridoxal 5'-phosphate as a cofactor
pyridoxal 5'-phosphate
-
-
pyridoxal 5'-phosphate
-
-
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
5,5'-dithiobis-(2-nitrobenzoic acid)
P25855
complete inhibition
aminoacetonitrile
P25855
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+
-
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
P25855
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
N-ethylmaleimide
-
-
N-ethylmaleimide
P25855
complete inhibition
N4-methylglutamine
-
inhibition of glycine-CO2 exchange reaction
Ni2+
-
inhibition of glycine-CO2 exchange by binding of metal with H-protein-bound intermediate of glycine decarboxylation
S-nitrosoglutathione
P25855
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
Modified H-protein
-
lipoic acid prosthetic group and cysteinyl residues modified with N-ethylmaleimide
-
additional information
-
inhibitors of the multienzyme complex
-
additional information
-
inactivation after incubation with glycine in presence of aminomethyl carrier protein (H-protein), it is a suicide reaction of the P-protein as a side reaction of the glycine decarboxylation
-
additional information
-
inhibitors of the multienzyme complex
-
additional information
-
low CO2 concentrations decrease expression of GDC
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
2-mercaptoethanol
-
thiol compound required for maximal activity on glycine-CO2 exchange reaction
dithiothreitol
-
P and H protein alone jointly catalyze the glycine-CO2 exchange reaction in presence of pyridoxal phosphate and dithiothreitol
dithiothreitol
-
thiol compound required for maximal activity on glycine-CO2 exchange reaction
GSH
-
thiol compound required for maximal activity on glycine-CO2 exchange reaction
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
31
-
bicarbonate
-
-
3.4
-
CO2
-
glycine-CO2 exchange
0.0034
-
glycine
-
-
0.0074
-
glycine
-
-
2.84
-
glycine
-
P-subunit in the absesence of H-apoprotein, at pH 6
2.92
-
glycine
-
P-subunit in the presence of non-tagged lipoylated H-apoprotein, at pH 8
2.93
-
glycine
-
P-subunit in the presence of His-tagged non-lipoylated H-apoprotein, at pH 6
3.05
-
glycine
-
P-subunit in the presence of His-tagged lipoylated H-apoprotein, at pH 6
3.14
-
glycine
-
P-subunit in the presence of His-tagged lipoylated H-apoprotein, at pH 8
3.21
-
glycine
-
P-subunit in the presence of non-tagged lipoylated H-apoprotein, at pH 6
5.8
-
glycine
-
-
6
-
glycine
C3-plants
-
-
6.6
-
glycine
-
-
20
-
glycine
-
glycine-CO2 exchange
32
-
glycine
-
-
40
-
glycine
-
-
0.0026
-
H1 protein
-
L protein
-
0.0037
-
H2 protein
-
L protein
-
12.3
-
His-tagged H-apoprotein
-
P-subunit, at pH 6
-
0.043
-
Lipoamide
-
the apparent Km-value of rTvL for binding the free lipoamide
0.47
-
lipoylated H-apoprotein
-
P-subunit, at pH 6
-
12.3
-
lipoylated H-apoprotein
-
P-subunit, at pH 8
-
1
-
lipoylated His-tagged H-apoprotein
-
P-subunit, at pH 6
-
12.6
-
lipoylated His-tagged H-apoprotein
-
P-subunit, at pH 8
-
0.0046
-
pyridoxal phosphate
-
-
0.0026
-
rTvH1 protein
-
the apparent Km-value of rTvL for binding rTvH1
-
0.0037
-
rTvH2 protein
-
the apparent Km-value of rTvL for binding rTvH2
-
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.602
-
Lipoamide
-
kinetic parameter for L protein
6.08
-
Lipoamide
-
kinetic parameter for L protein
0.84
-
rTvH1 protein
-
kinetic parameter for L protein
-
2.08
-
rTvH2 protein
-
kinetic parameter for L protein
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.02
-
-
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
0.25
-
-
-
4.13
-
-
-
additional information
-
-
mutations have a 6 to 8% of normal glycine decarboxylase activities when expressed in COS7 cells
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
6
-
-
P-subunit
6.6
-
-
glycine-CO2 exchange
6.7
-
-
glycine-CO2 exchange
7
-
-
glycine-CO2 exchange
7.1
-
-
glycine + lipoylprotein
7.4
-
-
assay condition for determination of the interaction of recombinant H an L protein
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
25
-
-
assay at
25
-
-
assay condition for determination of the interaction of recombinant H an L protein
37
-
-
assay at
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
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
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
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
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
-
-
predicted value TvH2 protein
15000
-
-
recombinant TvH2 protein, analysis of the native mass of TvH2 protein by gel filtration, SDS-PAGE and Western blot
51800
-
-
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
-
-
gel filtration
208000
-
-
sucrose density gradient centrifugation
210000
-
-
gel filtration
210000
-
-
sucrose density gradient centrifugation
215000
-
P74416
-
220000
-
-
SDS-PAGE
225000
-
-
gel filtration
270000
-
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
dimer
-
alpha2, 2 * 100000, SDS-PAGE
dimer
-
alpha2, 2 * 98000, SDS-PAGE
dimer
-
alpha2, 2 * 97000, lithium dodecyl sulfate PAGE
dimer
-
alpha2, 2 * 105000, SDS-PAGE
dimer
C3-plants
-
alpha2, 2 * 97000
dimer
P74416
-
heterotetramer
-
1 * 105000 + 1 * 60000 + 1 * 41000 + 1 * 14000, SDS-PAGE
homodimer
-
2 * 52000, SDS-PAGE, L protein
tetramer
-
alpha2beta2, 2 * 59500 + 2 * 54100, SDS-PAGE
tetramer
-
P, T, L and H protein
tetramer
-
T protein, P protein, H protein, L protein
monomer
-
1 * 14000, SDS-PAGE, H1 protein, 1 * 15000, SDS-PAGE, H2 protein
additional information
P25855
peptide mapping using trypsin degestion, overview
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
proteolytic modification
C3-plants
-
-
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
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
P74416
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
-
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
-
pH STABILITY
pH STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
6
8
-
P-subunit shows 50% lower activity at pH 8 than at pH 6
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
70
-
-
1 min, complete loss of activity
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-20C, several weeks
-
0-20C, 24 h, P-protein in purified P,L-protein fraction, 50-60% loss of activity
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
Q-Sepharose column chromatography and Sephacryl S-100 gel filtration
-
Ni-NTA column chromatography
P23434
recombinant His-tagged enzyme from Escherichia coli by nickel affinity and ion exchange chromatography, and gel filtration
P74416
H1, H2, and L protein purified to homogeneity, more than 95% pure; using a nickel-nitrilotriacetic acid-agarose column
-
ultracentrifugation
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expressed in Arabidopsis thaliana and Moricandia arvensis using Agrobacterium tumefaciens strain GV3101
-
expressed in Escherichia coli BL21(DE3) cells
-
expressed in Flaveria bidentis (C4) and Arabidopsis thaliana (C3)
-
expressed in Pichia pastoris strain GS115
P23434
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
-
expression of P-protein in yeast strains DS2-73U and DS2-75U
-
expressed in Escherichia coli strains BL21 Gold and LMG194
-
expression of the His-tagged enzyme in Escherichia coli
P74416
into pGEM-T vector for DNA manipulations and sequence analysis using the Escherichia coli strain TG1
-
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
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
A389V
-
missense mutation, 6-8% of normal GLDC activity when expressed in COS7 cells
Mu0171
-
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
-
knockout of glycine decarboxylase P-protein is lethal under nonphotorespiratory conditions
R739H
-
missense mutation, 6-8% of normal GLDC activity when expressed in COS7 cells
additional information
-
mutation of the genes for GDC subunits P, T, or H protein. No changes in growth, pigmentation, or photosynthesis in the GDC subunit mutants, regardless of whether or not cultivated at ambient or high CO2 concentrations. Mutation of GDC leads to an increased glycine/serine ratio in the mutant cells. Supplementation of the medium with low glycine concentrations is toxic for the mutants but not for wild-type cells
additional information
-
mutant affected in T-protein subunit of GDC shows similar CO2-dependent regulation as wild-type cells. Glycine decarboxylase knockout mutants exposed to low CO2 accumulate far more glycine and lysine than wild-type cells or mutants with inactivated glycerate pathway
additional information
-
inactivation of the sll0171 gene by introducing a spectinomycin-resistance cartridge
APPLICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
medicine
-
mutations of the glycine decarboxylase gene are found in patients with nonketotic hyperglycinemia, NKH
additional information
-
GDC is not necessary for cell viability under standard conditions. GDC is dispensable for Synechocystis
additional information
-
GDC is dispensable for cyanobacterial metabolism