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Information on EC 2.1.1.20 - glycine N-methyltransferase and Organism(s) Rattus norvegicus and UniProt Accession P13255

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EC Tree
     2 Transferases
         2.1 Transferring one-carbon groups
             2.1.1 Methyltransferases
                2.1.1.20 glycine N-methyltransferase
IUBMB Comments
This enzyme is thought to play an important role in the regulation of methyl group metabolism in the liver and pancreas by regulating the ratio between S-adenosyl-L-methionine and S-adenosyl-L-homocysteine. It is inhibited by 5-methyltetrahydrofolate pentaglutamate . Sarcosine, which has no physiological role, is converted back into glycine by the action of EC 1.5.8.3, sarcosine dehydrogenase.
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Rattus norvegicus
UNIPROT: P13255
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Word Map
The taxonomic range for the selected organisms is: Rattus norvegicus
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
Synonyms
gnmt, glycine n-methyltransferase, glycine methyltransferase, s-adenosyl-l-methionine:glycine n-methyltransferase, glycine-n methyltransferase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
glycine methyltransferase
-
glycine methyltransferase
-
-
-
-
methyltransferase, glycine
-
-
-
-
S-adenosyl-L-methionine:glycine methyltransferase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + glycine = S-adenosyl-L-homocysteine + sarcosine
show the reaction diagram
mechanism
S-adenosyl-L-methionine + glycine = S-adenosyl-L-homocysteine + sarcosine
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
methyl group transfer
-
-
-
-
PATHWAY SOURCE
PATHWAYS
-
-, -
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:glycine N-methyltransferase
This enzyme is thought to play an important role in the regulation of methyl group metabolism in the liver and pancreas by regulating the ratio between S-adenosyl-L-methionine and S-adenosyl-L-homocysteine. It is inhibited by 5-methyltetrahydrofolate pentaglutamate [4]. Sarcosine, which has no physiological role, is converted back into glycine by the action of EC 1.5.8.3, sarcosine dehydrogenase.
CAS REGISTRY NUMBER
COMMENTARY hide
37228-72-1
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + glycine
S-adenosyl-L-homocysteine + N-methylglycine
show the reaction diagram
S-adenosyl-L-methionine + glycine
S-adenosyl-L-homocysteine + sarcosine
show the reaction diagram
S-adenosyl-L-methionine + glycine
S-adenosyl-L-homocysteine + N-methylglycine
show the reaction diagram
S-adenosyl-L-methionine + glycine
S-adenosyl-L-homocysteine + sarcosine
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + glycine
S-adenosyl-L-homocysteine + N-methylglycine
show the reaction diagram
S-adenosyl-L-methionine + glycine
S-adenosyl-L-homocysteine + N-methylglycine
show the reaction diagram
-
key enzyme for the regulation of the ratio of S-adenosylmethionine to S-adenosylhomocysteine
N-methylglycine = sarcosine
-
?
S-adenosyl-L-methionine + glycine
S-adenosyl-L-homocysteine + sarcosine
show the reaction diagram
additional information
?
-
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5-methyltetrahydrofolate
-
5-Methyltetrahydrofolate pentaglutamate
-
folate
the native rat liver GNMT contains an acetylated N-terminal valine and is inhibited much more efficiently compared to the recombinant protein
S-adenosyl-L-homocysteine
weak
5'-[p-(fluorosulfonyl)benzoyl]adenosine
-
-
5,5'-dithiobis(2-nitrobenzoate)
-
-
5-methyl-tetrahydrofolate
-
-
5-Methyltetrahydrofolate hexaglutamate
-
-
5-methyltetrahydrofolate monoglutamate
-
native N-acetylated form of the enzyme shows 50% inhibition at 0.05 mM while the recombinant non-acetylated form shows 50% inhibition at 1.89 mM
5-Methyltetrahydrofolate pentaglutamate
5-Methyltetrahydrofolate triglutamate
-
-
5-methyltetrahydrofolic acid
-
-
5-Methyltetrahydropteroylpentaglutamate
-
-
folinic acid
-
-
iodoacetate
-
-
methotrexate
-
-
additional information
-
folate-containing diets attenuate GNMT activity in diabetic rats but are without effect on abundance
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
glucagon
GNMT activity is induced by glucagon
Vitamin A
GNMT activity is induced by vitamin A
glucagon
-
elevates GNMT activity
phosphate
-
in vitro phosphorylation increases activity, about 0.55 mol of phosphate present per mol of N-methyltransferase subunit
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.24 - 30
Gly
1.1 - 38.8
glycine
0.014 - 1.136
S-adenosyl-L-methionine
0.13 - 1.9
glycine
0.03
S-adenosylmethionine
-
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.105 - 0.47
Gly
0.0097 - 2.908
S-adenosyl-L-methionine
0.7 - 51.9
glycine
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0003 - 2.616
glycine
0.012 - 26.935
S-adenosyl-L-methionine
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0013 - 0.59
5-Methyltetrahydrofolate pentaglutamate
0.001 - 0.002
5-Methyltetrahydrofolate pentaglutamate
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
-
assay pH
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
-
assay temperature
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
presence in liver nuclei
Manually annotated by BRENDA team
additional information
-
overview on subcellular localization
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
GNMT is involved in both hepatic methyl group and one-carbon metabolism
physiological function
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
GNMT_RAT
293
0
32549
Swiss-Prot
other Location (Reliability: 2)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
32500
4 * 32500
130000
130000 - 132000
-
sedimenation equilibrium centrifugation, gel filtration
135000
-
gel filtration
31500
-
4 * 31500, identical subunits, SDS-PAGE
32420 - 79000
-
mass spectrometry, mass spectra of the proteins greatly depend on the method of sample preparation and storage
32500
34000
-
x * 34000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homotetramer
4 * 32500
tetramer
?
-
x * 34000, SDS-PAGE
homotetramer
-
4 * 32500
tetramer
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
acetylated protein
-
N-terminal valine of native GNMT is N-acetylated while in the recombinant enzyme it is not
phosphoprotein
-
GNMT is phosphorylated by cAMP-dependent protein kinase at Ser9, Ser71, Ser139, Ser182, and Ser241
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystallized by the sitting drop method in complex with (6S)-5-methyltetrahydrofolat monoglutamate
GNMT complexed with 5-methyltetrahydrofolate, by the sitting drop method at room temperature, two folate binding sites in the intersubunit areas of the tetramer, each folate binding site is formed primarily by two 1-7 N-terminal regions of one pair of subunits and two 205-218 regions of the other pair of subunits. Both the pteridine and p-aminobenzoyl rings are located in the hydrophobic cavities formed by Tyr5, Leu207, and Met215 residues of all subunits
hanging drop method of vapor diffusion, crystal structure of the enzyme complexed with S-adenosyl-L-methionine and acetate (a potent competitive inhibitor of Gly) and the R175K mutated enzyme complexed with S-adenosyl-L-methionine are determined at 2.8 A and 3.0 A resolution, respectively
including R175K mutant
native and recombinant protein, to 2.55 A resolution. The native rat liver GNMT contains an acetylated N-terminal valine and is inhibited much more efficiently compared to the recombinant protein. In the folate-GNMT complexes with the native enzyme, two folate molecules establish three and four hydrogen bonds with the protein. In the folate-recombinant GNMT complex only one hydrogen bond is established. This difference results in more effective inhibition by folate of the native liver GNMT activity compared to the recombinant enzyme
sitting-drop vapor diffusion method in complex with 5-methyltetrahydrofolate pentaglutamate, two molecules of inhibitor bound to a tetramer
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
R175K
crystal structure: N-terminal domains of subunits have moved out of the active sites of adjacent subunits
Y194F
the ratio of turnover-number to KM-value for S-adenosyl-L-methionine is 2.4fold lower than the wild-type value, the ratio of turnover-number to KM-value for Gly is 16.4fold lower than the wild-type value
Y21S
mutant yields the same magnitude of binary isotope effect as wild-type
Y21T
mutant yields the same magnitude of binary isotope effect as wild-type
Y21V
mutant yields the same magnitude of binary isotope effect as wild-type
Y220F
the ratio of turnover-number to KM-value for S-adenosyl-L-methionine is nearly identical to the wild-type value, the ratio of turnover-number to KM-value for Gly is 179fold lower than the wild-type value
Y242F
the ratio of turnover-number to KM-value for S-adenosyl-L-methionine is 1.14fold higher than the wild-type value, the ratio of turnover-number to KM-value for Gly is 2325fold lower than the wild-type value
Y33F
the ratio of turnover-number to KM-value for S-adenosyl-L-methionine is nearly identical to the wild-type value, the ratio of turnover-number to KM-value for Gly is 123fold lower than the wild-type value
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, 5.0 mM DTT, 2.0 mM EDTA, 0.02% NaN3, stable for at least 2 weeks
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
by ammonium sulfate precipitation and gel filtration
recombinant protein
from liver by anion and cation exchange chromatography and from isolated hepatocytes and liver tissue by immunoprecipitation
-
native enzyme from rat liver and recombinant enzyme from Escherichia coli
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
expressed in Escherichia coli BL21(DE3)
expressed in Escherichia coli BL21(GE3)
expression in Escherichia coli
into pET-17b vector and expressed in Escherichia coli BL21(GE3)
expressed in Escherichia coli
-
when expressed in pTYB vector as a fusion protein with intein and the chitin binding domain, a cleavage of intein is found. The cleavage takes place at two sites near the N-terminus of intein and results in the appearance of an abnormal GNMT protein after one-column cleavage of the fusion protein, which can not be separated from normal GNMT. For this reason expression is done in the vector pET-17b. Expression of soluble protein in Escherichia coli at about 20-40 mg/L
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
GNMT expression is down-regulated or even completely blocked in liver and prostate tumor tissue
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
additional information
-
phosphorylated serine residues 71, 182, and 241, in GNMT prepared from liver tissue and hepatocytes an S9 additional residue is phosphorylated, in hepatocytes and in recombinant GNMT S139 is detected, serine 9 is also identified as a target for cAMP-dependent protein kinase in vitro, positions of these phosphorylated residues in the tertiary structure of GNMT indicate their possible effect on enzyme conformation and activity
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Wagner, C.; Decha-Umphai, W.; Corbin, J.
Phosphorylation modulates the activity of glycine N-methyltransferase, a folate binding protein. In vitro phosphorylation is inhibited by the natural folate ligand
J. Biol. Chem.
264
9638-9642
1989
Rattus norvegicus
Manually annotated by BRENDA team
Ogawa, H.; Fujioka, M.
Purification and properties of glycine N-methyltransferase from rat liver
J. Biol. Chem.
257
3447-3452
1982
Rattus norvegicus
Manually annotated by BRENDA team
Fujioka, M.; Ishiguro, Y.
Reaction of rat liver glycine methyltransferase with 5-p-fluorosulfonylbenzoyladenosine
J. Biol. Chem.
261
6346-6351
1986
Rattus norvegicus
Manually annotated by BRENDA team
Yeo, E.J.; Wagner, C.
Purification and properties of pancreatic glycine N-methyltransferase
J. Biol. Chem.
267
24669-24674
1992
Rattus norvegicus
Manually annotated by BRENDA team
Fujioka, M.; Takata, Y.; Konishi, K.; Ogawa, H.
Function and reactivity of sulfhydryl groups of rat liver glycine methyltransferase
Biochemistry
26
5696-5702
1987
Rattus norvegicus
Manually annotated by BRENDA team
Wagner, C.; Briggs, W.T.; Cook, R.J.
Inhibition of glycine N-methyltransferase activity by folate derivatives: implications for regulation of methyl group metabolism
Biochem. Biophys. Res. Commun.
127
746-752
1985
Rattus norvegicus
Manually annotated by BRENDA team
Pattanayek, R.; Newcomer, M.E.; Wagner, C.
Crystal structure of apo-glycine N-methyltransferase (GNMT)
Protein Sci.
7
1326-1331
1998
Rattus norvegicus
Manually annotated by BRENDA team
Fu, Z.; Hu, Y.; Konishi, K.; Takata, Y.; Ogawa, H.; Gomi, T.; Fujioka, M.; Takusagawa, F.
Crystal structure of glycine N-methyltransferase from rat liver
Biochemistry
35
11985-11993
1996
Rattus norvegicus (P13255)
Manually annotated by BRENDA team
Huang, Y.; Komoto, J.; Konishi, K.; Takata, Y.; Ogawa, H.; Gomi, T.; Fujioka, M.; Takusagawa, F.
Mechanisms for auto-inhibition and forced product release in glycine N-methyltransferase: Crystal structures of wild-type, mutant R175K and S-adenosylhomocysteine-bound R175K enzymes
J. Mol. Biol.
298
149-162
2000
Rattus norvegicus (P13255)
Manually annotated by BRENDA team
Bhat, R.; Bresnick, E.
Glycine N-methyltransferase is an example of functional diversity. Role as a polycyclic aromatic hydrocarbon-binding receptor
J. Biol. Chem.
272
21221-21226
1997
Rattus norvegicus
Manually annotated by BRENDA team
Bhat, R.; Wagner, C.; Bresnick, E.
The homodimeric form of glycine N-methyltransferase acts as a polycyclic aromatic hydrocarbon-binding receptor
Biochemistry
36
9906-9910
1997
Rattus norvegicus
Manually annotated by BRENDA team
Ogawa, H.; Gomi, T.; Imamura, T.; Kobayashi, M.; Huh, N.H.
Rat liver 4 S-benzo[a]pyrene-binding protein is distinct from glycine N-methyltransferase
Biochem. Biophys. Res. Commun.
233
300-304
1997
Rattus norvegicus
Manually annotated by BRENDA team
Raha, A.; Wagner, C.; MacDonald, R.G.; Bresnick, E.
Rat liver cytosolic 4 S polycyclic aromatic hydrocarbon-binding protein is glycine N-methyltransferase
J. Biol. Chem.
269
5750-5756
1994
Rattus norvegicus
Manually annotated by BRENDA team
Ogawa, H.; Gomi, T.; Takusagawa, F.; Fujioka, M.
Structure, function and physiological role of glycine N-methyltransferase
Int. J. Biochem. Cell Biol.
30
13-26
1998
Homo sapiens, Mus musculus, Oryctolagus cuniculus, Rattus norvegicus
Manually annotated by BRENDA team
Rowling, M.J.; McMullen, M.H.; Schalinske, K.L.
Vitamin A and its derivatives induce hepatic glycine N-methyltransferase and hypomethylation of DNA in rats
J. Nutr.
132
365-369
2002
Rattus norvegicus
Manually annotated by BRENDA team
Rowling, M.J.; McMullen, M.H.; Chipman, D.C.; Schalinske, K.L.
Hepatic glycine N-methyltransferase is up-regulated by excess dietary methionine in rats
J. Nutr.
132
2545-2550
2002
Rattus norvegicus
Manually annotated by BRENDA team
Yeo, E.J.; Wagner, C.
Tissue distribution of glycine N-methyltransferase, a major folate-binding protein of liver
Proc. Natl. Acad. Sci. USA
91
210-214
1994
Rattus norvegicus
Manually annotated by BRENDA team
McMullen, M.H.; Rowling, M.J.; Ozias, M.K.; Schalinske, K.L.
Activation and induction of glycine N-methyltransferase by retinoids are tissue- and gender-specific
Arch. Biochem. Biophys.
401
73-80
2002
Rattus norvegicus
Manually annotated by BRENDA team
Takata, Y.; Huang, Y.; Komoto, J.; Yamada, T.; Konishi, K.; Ogawa, H.; Gomi, T.; Fujioka, M.; Takusagawa, F.
Catalytic mechanism of glycine N-methyltransferase
Biochemistry
42
8394-8402
2003
Rattus norvegicus (P13255)
Manually annotated by BRENDA team
Rowling, M.J.; Schalinske, K.L.
Retinoic acid and glucocorticoid treatment induce hepatic glycine N-methyltransferase and lower plasma homocysteine concentrations in rats and rat hepatoma cells
J. Nutr.
133
3392-3398
2003
Rattus norvegicus
Manually annotated by BRENDA team
Ozias, M.K.; Schalinske, K.L.
All-trans-retinoic acid rapidly induces glycine N-methyltransferase in a dose-dependent manner and reduces circulating methionine and homocysteine levels in rats
J. Nutr.
133
4090-4094
2003
Rattus norvegicus
Manually annotated by BRENDA team
Luka, Z.; Wagner, C.
Expression and purification of glycine N-methyltransferases in Escherichia coli
Protein Expr. Purif.
28
280-286
2003
Homo sapiens, Mus musculus, Rattus norvegicus
Manually annotated by BRENDA team
Nieman, K.M.; Hartz, C.S.; Szegedi, S.S.; Garrow, T.A.; Sparks, J.D.; Schalinske, K.L.
Folate status modulates the induction of hepatic glycine N-methyltransferase and homocysteine metabolism in diabetic rats
Am. J. Physiol. Endocrinol. Metab.
291
E1235-E1242
2006
Rattus norvegicus
Manually annotated by BRENDA team
Luka, Z.; Pakhomova, S.; Loukachevitch, L.V.; Egli, M.; Newcomer, M.E.; Wagner, C.
5-methyltetrahydrofolate is bound in intersubunit areas of rat liver folate-binding protein glycine N-methyltransferase
J. Biol. Chem.
282
4069-4075
2007
Rattus norvegicus (P13255)
Manually annotated by BRENDA team
Luka, Z.; Ham, A.J.; Norris, J.L.; Yeo, E.J.; Yermalitsky, V.; Glenn, B.; Caprioli, R.M.; Liebler, D.C.; Wagner, C.
Identification of phosphorylation sites in glycine N-methyltransferase from rat liver
Protein Sci.
15
785-794
2006
Rattus norvegicus
Manually annotated by BRENDA team
Luka, Z.; Loukachevitch, L.V.; Wagner, C.
Acetylation of N-terminal valine of glycine N-methyltransferase affects enzyme inhibition by folate
Biochim. Biophys. Acta
1784
1342-1346
2008
Rattus norvegicus
Manually annotated by BRENDA team
Luka, Z.; Mudd, S.H.; Wagner, C.
Glycine N-methyltransferase and regulation of S-adenosylmethionine levels
J. Biol. Chem.
284
22507-22511
2009
Danio rerio, Oryctolagus cuniculus, Homo sapiens, Mus musculus, Sus scrofa, Rattus norvegicus (P13255)
Manually annotated by BRENDA team
Luka, Z.
Methyltetrahydrofolate in folate-binding protein glycine N-methyltransferase
Vitam. Horm.
79
325-345
2008
Oryctolagus cuniculus, Homo sapiens, Rattus norvegicus, Sus scrofa (Q29555), Mus musculus (Q9QXF8), Mus musculus
Manually annotated by BRENDA team
Luka, Z.; Pakhomova, S.; Loukachevitch, L.; Newcomer, M.; Wagner, C.
Differences in folate-protein interactions result in differing inhibition of native rat liver and recombinant glycine N-methyltransferase by 5-methyltetrahydrofolate
Biochim. Biophys. Acta
1824
286-291
2012
Rattus norvegicus (P13255)
Manually annotated by BRENDA team
Zhang, J.; Klinman, J.P.
Convergent mechanistic features between the structurally diverse N- and O-methyltransferases glycine N-methyltransferase and catechol O-methyltransferase
J. Am. Chem. Soc.
138
9158-9165
2016
Rattus norvegicus (P13255)
Manually annotated by BRENDA team
Swiderek, K.; Tunon, I.; Williams,I. H.; Moliner, V.
Insights on the origin of catalysis on glycine N-methyltransferase from computational modeling
J. Am. Chem. Soc.
140
4327-4334
2018
Rattus norvegicus (P13255)
Manually annotated by BRENDA team