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Information on EC 1.4.4.2 - glycine dehydrogenase (aminomethyl-transferring) and Organism(s) Synechocystis sp. and UniProt Accession P74416
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1.4.4.2 glycine dehydrogenase (aminomethyl-transferring)IUBMB Comments
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 . Previously known as glycine synthase.
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- 1.4.4.2
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coil
- aneurysm
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guglielmi
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embolization
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endovascular
- artery
- measles
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occlusion
- cerebral
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intracranial
- hemagglutinin
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rupture
- neck
-
dental
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subarachnoid
- hemorrhage
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photorespiratory
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angiographic
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photorespiration
-
council
- distemper
- hyperglycinemia
-
dentist
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lipoylation
- hydroxymethyltransferase
- polyomavirus
-
angiogram
-
t-proteins
-
slam
-
lipoic
-
nonketotic
-
rebleeding
-
microcatheter
- morbillivirus
- vasospasm
-
unruptured
-
recanalization
-
basilar
-
polyoma
-
ceria
- glycodeoxycholate
-
practise
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procedure-related
- lipoamide
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profession
- flaveria
- lipoate
- panencephalitis
- medicine
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postal
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curriculum
The taxonomic range for the selected organisms is: Synechocystis sp.
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
Synonyms
gdc, h protein, h-protein, glycine decarboxylase, t protein, protein p1, h1 protein, glycine decarboxylase complex, glycine cleavage enzyme complex, h2 protein, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
decarboxylase, glycine
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Glycine cleavage system P-protein
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-
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glycine decarboxylase
glycine decarboxylase P-protein
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glycine dehydrogenase (decarboxylating)
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-
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glycine-cleavage complex
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P-protein
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-
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Protein P1
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-
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additional information
glycine decarboxylase, or P-protein, is part of the glycine cleavage system, GCS
glycine decarboxylase
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-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
decarboxylation
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-
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redox reaction
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-
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oxidation
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reduction
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PATHWAY SOURCE
PATHWAYS
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-, -
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
37259-67-9
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
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-
-
?
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
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
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?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
glycine + H-protein-lipoyllysine
H-protein-S-aminomethyldihydrolipoyllysine + CO2
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
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?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pyridoxal 5'-phosphate
P-protein is the actual glycine-decarboxylating enzyme and uses pyridoxal 5'-phosphate as a cofactor
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
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low CO2 concentrations decrease expression of GDC
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2.92
glycine
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P-subunit in the presence of non-tagged lipoylated H-apoprotein, at pH 8
2.93
glycine
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P-subunit in the presence of His-tagged non-lipoylated H-apoprotein, at pH 6
3.05
glycine
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P-subunit in the presence of His-tagged lipoylated H-apoprotein, at pH 6
3.14
glycine
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P-subunit in the presence of His-tagged lipoylated H-apoprotein, at pH 8
3.21
glycine
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P-subunit in the presence of non-tagged lipoylated H-apoprotein, at pH 6
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
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
additional information
additional information
glycine decarboxylase, or P-protein, is part of the glycine cleavage system, GCS
additional information
-
glycine decarboxylase, or P-protein, is part of the glycine cleavage system, GCS
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant His-tagged enzyme, hanging drop vapour diffusion, 18°C, 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 20°C, X-ray diffraction structure determination and analysis at 2.1 A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
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
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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
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli by nickel affinity and ion exchange chromatography, and gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
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GDC is not necessary for cell viability under standard conditions. GDC is dispensable for Synechocystis
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Hagemann, M.; Vinnemeier, J.; Oberpichler, I.; Boldt, R.; Bauwe, H.
The glycine decarboxylase complex is not essential for the cyanobacterium Synechocystis sp. strain PCC 6803
Plant Biol.
7
15-22
2005
Synechocystis sp., Synechocystis sp. PCC 6803
Eisenhut, M.; Kahlon, S.; Hasse, D.; Ewald, R.; Lieman-Hurwitz, J.; Ogawa, T.; Ruth, W.; Bauwe, H.; Kaplan, A.; Hagemann, M.
The plant-like C2 glycolate cycle and the bacterial-like glycerate pathway cooperate in phosphoglycolate metabolism in cyanobacteria
Plant Physiol.
142
333-342
2006
Synechocystis sp., Synechocystis sp. PCC 6803
Hasse, D.; Mikkat, S.; Thrun, H.A.; Hagemann, M.; Bauwe, H.
Properties of recombinant glycine decarboxylase P- and H-protein subunits from the cyanobacterium Synechocystis sp. strain PCC 6803
FEBS Lett.
581
1297-1301
2007
Synechocystis sp.
Hasse, D.; Hagemann, M.; Andersson, I.; Bauwe, H.
Crystallization and preliminary X-ray diffraction analyses of the homodimeric glycine decarboxylase (P-protein) from the cyanobacterium Synechocystis sp. PCC 6803
Acta Crystallogr. Sect. F
66
187-191
2010
Synechocystis sp. (P74416), Synechocystis sp.
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