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Information on EC 2.1.2.10 - aminomethyltransferase and Organism(s) Homo sapiens and UniProt Accession P48728

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IUBMB Comments
A component, with EC 1.4.4.2 glycine dehydrogenase (decarboxylating) and EC 1.8.1.4, dihydrolipoyl dehydrogenanse, of the glycine cleavage system, formerly known as glycine synthase. The glycine cleavage system 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), the L protein (EC 1.8.1.4) and the lipoyl-bearing H protein .
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Homo sapiens
UNIPROT: P48728
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The taxonomic range for the selected organisms is: Homo sapiens
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
aminomethyltransferase, glycine synthase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
aminomethyltransferase
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glycine synthase
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-
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synthase, glycine
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-
-
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T protein
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-
-
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T-protein
tetrahydrofolate aminomethyltransferase
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-
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-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
[protein]-S8-aminomethyldihydrolipoyllysine + tetrahydrofolate = [protein]-dihydrolipoyllysine + 5,10-methylenetetrahydrofolate + NH3
show the reaction diagram
5-methyltetrahydrofolate is bound in a kinked shape with the pteridine group deeply buried into the hydrophobic pocket ant the glutamyl group pointed to the C-terminal side surface. R292 interacts through water molecules with the folate polyglutamate tail
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
methyl group transfer
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C-N bond cleavage
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SYSTEMATIC NAME
IUBMB Comments
[protein]-S8-aminomethyldihydrolipoyllysine:tetrahydrofolate aminomethyltransferase (ammonia-forming)
A component, with EC 1.4.4.2 glycine dehydrogenase (decarboxylating) and EC 1.8.1.4, dihydrolipoyl dehydrogenanse, of the glycine cleavage system, formerly known as glycine synthase. The glycine cleavage system 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), the L protein (EC 1.8.1.4) and the lipoyl-bearing H protein [3].
CAS REGISTRY NUMBER
COMMENTARY hide
37257-08-2
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
[protein]-S8-aminomethyldihydrolipoyllysine + tetrahydrofolate
[protein]-dihydrolipoyllysine + 5,10-methylenetetrahydrofolate + NH3
show the reaction diagram
-
-
-
?
S-aminomethyldihydrolipoylprotein + (6S)-tetrahydrofolate
dihydrolipoylprotein + (6R)-5,10-methylenetetrahydrofolate + NH3
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
[protein]-S8-aminomethyldihydrolipoyllysine + tetrahydrofolate
[protein]-dihydrolipoyllysine + 5,10-methylenetetrahydrofolate + NH3
show the reaction diagram
-
-
-
?
S-aminomethyldihydrolipoylprotein + (6S)-tetrahydrofolate
dihydrolipoylprotein + (6R)-5,10-methylenetetrahydrofolate + NH3
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
tetrahydrofolate
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requires tetrahydrofolate
additional information
-
H-protein with reduced lipoate
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
required
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
Uniprot
Manually annotated by BRENDA team
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
mutations S117L and R320H cause nonketotic hyperglycinemia (NKH). Analysis of mutations in the GLYCTK gene (encoding D-glycerate kinase, EC 2.7.1.165) causing glyceric aciduria. D-glyceric aciduria causes a blockage to the glycine cleavage enzyme system (GCS). The mutation S117L, a homozygous missense mutation in AMT c.350CNT, causes NKH, but no evidence is found that D-glyceric aciduria would cause nonketotic hyperglycinemia (NKH) as a secondary phenomenon. The p.Arg320His is included as the most common AMT mutation observed in NKH patients and when homozygous, is always observed in a severe phenotype
malfunction
physiological function
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part of glycine cleavage system, serine metabolism
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
GCST_HUMAN
403
0
43946
Swiss-Prot
Mitochondrion (Reliability: 1)
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
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-
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
apoform and bound to 5-methyltetrahydrofolate
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
F483S
naturally occuring mutation that causes D-glyceric aciduria
R320H
naturally occuring mutation that causes D-glyceric aciduria, the mutant enzyme shows 13% activity compared to wild-type. The expression of the p.Arg320Hisu mutant shows a low residual enzyme activity of the glycine cleavage enzyme similar to that of the mock control. The p.Arg320His is included as the most common AMT mutation observed in NKH patients and when homozygous, is always observed in a severe phenotype
S117L
naturally occuring mutation, a very rare homozygous missense mutation in AMT c.350CNT, that causes D-glyceric aciduria, but no evidence is found that D-glyceric aciduria would cause nonketotic hyperglycinemia (NKH) as a secondary phenomenon. The mutant enzyme shows 9% activity compared to wild-type. The expression of the p.Ser117Leu mutant shows a low residual enzyme activity of the glycine cleavage enzyme similar to that of the mock control
D276H
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nonketotic hyperglycinemia, rare mutation
E211K
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polymorphism occurring in patients with glycine encephalopathy, NKH, method for PCR-restriction enzyme analysis
G269D
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nonketotic hyperglycinemia, rare mutation
G47R
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nonketotic hyperglycinemia, rare mutation
H42R
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present in many nonketotic hyperglycinemia affected members of an extended Israeli-Arab kindred
N117I
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mutant may cause nonketotic hygerglycinemia
N145I
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nonketotic hyperglycinemia, substitution of conserved N, patient has servere neonatal presentation and died in the newborn period
Q189*
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the mutation causes nonketotic hyperglycinemia
Q192X
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nonketotic hyperglycinemia, premature stop codon
R265H
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naturally occurring mutation in glycine encephalopathy patients and the Penan sub-population. Detection of four missense mutations (c.664C4T, c.688G4C, c.794G4A, c.826G4C) and one heterozygous deletion causing frameshift mutation (c.982delG) in AMT gene
R296H
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mutation occurring in patients with glycine encephalopathy, NKH, method for PCR-restriction enzyme analysis
R318R
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polymorphism occurring in patients with glycine encephalopathy, NKH, method for PCR-restriction enzyme analysis
R320H
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allele frequency of 7% for R320H of T-protein in 50 patients with enzymatic confirmation of their diagnostics of nonketotic hyperglycinemia
additional information
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene AMT, located on chromosome 3p21.3, DNA and amino acid sequence determination and analysis. The AMT gene is located on chromosome 3p21.3 and the GLYCTK gene on 3p21.1. The possibility of a microdeletion is considered given the homozygosity for a mutation in both genes in a non-consanguineous family, but a comparative microarray does not identify a copy number variation in any exon of either gene
Amt gene is located on chromosome 3p21 and contains 9 exons spanning about 6 kb of genomic sequence
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gene AMT, genotyping in 14 glycine encephalopathy patients from 13 families from Malaysia, six patients (43%) have biallelic mutations in the AMT gene
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Toone, J.R.; Applegarth, D.A.; Coulter-Mackie, M.B.; James, E.R.
Recurrent mutations in P- and T-proteins of the glycine cleavage complex and a novel T-protein mutation (N145I): A strategy for the molecular investigation of patients with nonketotic hyperglycinemia (NKH)
Mol. Genet. Metab.
72
322-325
2001
Homo sapiens
Manually annotated by BRENDA team
Backofen, B.; Leeb, T.
Genomic organization of the murine aminomethyltransferase gene (Amt)
DNA Seq.
13
179-183
2002
Homo sapiens, Mus musculus
Manually annotated by BRENDA team
Okamura-Ikeda, K.; Hosaka, H.; Yoshimura, M.; Yamashita, E.; Toma, S.; Nakagawa, A.; Fujiwara, K.; Motokawa, Y.; Taniguchi, H.
Crystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia
J. Mol. Biol.
351
1146-1159
2005
Homo sapiens (P48728)
Manually annotated by BRENDA team
Toone, J.R.; Applegarth, D.A.; Levy, H.L.; Coulter-Mackie, M.B.; Lee, G.
Molecular genetic and potential biochemical characteristics of patients with T-protein deficiency as a cause of glycine encephalopathy (NKH)
Mol. Genet. Metab.
79
272-280
2003
Homo sapiens
Manually annotated by BRENDA team
Kikuchi, G.; Motokawa, Y.; Yoshida, T.; Hiraga, K.
Glycine cleavage system: reaction mechanism, physiological significance, and hyperglycinemia
Proc. Jpn. Acad. Ser. B Phys. Biol. Sci.
84
246-263
2008
Escherichia coli, Homo sapiens, Pisum sativum
Manually annotated by BRENDA team
Azize, N.A.; Ngah, W.Z.; Othman, Z.; Md Desa, N.; Chin, C.B.; Md Yunus, Z.; Mohan, A.; Hean, T.S.; Syed Zakaria, S.Z.; Lock-Hock, N.
Mutation analysis of glycine decarboxylase, aminomethyltransferase and glycine cleavage system protein-H genes in 13 unrelated families with glycine encephalopathy
J. Hum. Genet.
59
593-597
2014
Homo sapiens
Manually annotated by BRENDA team
Gencpinar, P.; Cavusoglu, D.; Oezbeyler, O.e.; Kaya, O.O.; Baydan, F.; Olgac Dundar, N.
Nonketotic hyperglycinemia novel mutation in the aminomethyl transferase gene. Case report
Arch. Argent. Pediatr.
114
e142-e146
2016
Homo sapiens
Manually annotated by BRENDA team
Swanson, M.A.; Garcia, S.M.; Spector, E.; Kronquist, K.; Creadon-Swindell, G.; Walter, M.; Christensen, E.; Van Hove, J.L.K.; Sass, J.O.
D-Glyceric aciduria does not cause nonketotic hyperglycinemia a historic co-occurrence
Mol. Genet. Metab.
121
80-82
2017
Homo sapiens (P48728)
Manually annotated by BRENDA team