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Literature summary extracted from

  • 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 (2017), Mol. Genet. Metab., 121, 80-82 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.1.2.10 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 Homo sapiens
2.7.1.31 gene GLYCTK, located on chromosome 3p21.1, 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 Homo sapiens

Protein Variants

EC Number Protein Variants Comment Organism
2.1.2.10 F483S naturally occuring mutation that causes D-glyceric aciduria Homo sapiens
2.1.2.10 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 Homo sapiens
2.1.2.10 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 Homo sapiens
2.7.1.31 F483S naturally occuring mutation, the homozygous mutation c.1448delT, p.Phe483SerfsX2 in the GLYCTK gene causes D-glyceric aciduria, but is not involved in nonketotic hyperglycinemia (NKH) as a secondary phenomenon, the latter is caused by mutations in the AMT gene (EC 2.1.2.10), also harbored by the patient Homo sapiens

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.1.2.10 Mg2+ required Homo sapiens
2.7.1.31 Mg2+ required Homo sapiens

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.1.2.10 [protein]-S8-aminomethyldihydrolipoyllysine + tetrahydrofolate Homo sapiens
-
 [protein]-dihydrolipoyllysine + 5,10-methylenetetrahydrofolate + NH3
-
 ?
2.7.1.31 ATP + D-glycerate Homo sapiens
-
 ADP + phospho-D-glycerate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.1.2.10 Homo sapiens P48728
-
-
2.7.1.31 Homo sapiens Q8IVS8
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.1.2.10 [protein]-S8-aminomethyldihydrolipoyllysine + tetrahydrofolate
-
 Homo sapiens [protein]-dihydrolipoyllysine + 5,10-methylenetetrahydrofolate + NH3
-
 ?
2.7.1.31 ATP + D-glycerate
-
 Homo sapiens ADP + phospho-D-glycerate
-
 ?
2.7.1.31 ATP + D-glycerate the position of phosphorylation on D-glycerate is not specified in the publication, cf. EC 2.7.1.165 Homo sapiens ADP + phospho-D-glycerate
-
 ?

Synonyms

EC Number Synonyms Comment Organism
2.1.2.10 Amt
-
 Homo sapiens
2.7.1.31 D-glycerate kinase
-
 Homo sapiens
2.7.1.31 GLYCTK gene
-
 Homo sapiens
2.7.1.31 More cf. EC 2.7.1.165 Homo sapiens

General Information

EC Number General Information Comment Organism
2.1.2.10 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 Homo sapiens
2.7.1.31 malfunction a mutation in the GLYCTK gene encoding D-glycerate kinase causes glyceric aciduria. D-glyceric aciduria causes a blockage to the glycine cleavage enzyme system (GCS). The mutation S117L, a homozygous missense mutation in aminomethyltransferase (AMT, EC 2.1.2.10), causes nonketotic hyperglycinemia (NKH), but no evidence is found that D-glyceric aciduria would cause nonketotic hyperglycinemia (NKH) as a secondary phenomenon. The AMT p.Arg320His mutation is included as the most common AMT mutation observed in NKH patients and when homozygous, is always observed in a severe phenotype Homo sapiens