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Literature summary for 1.4.4.2 extracted from

  • Go, M.K.; Zhang, W.C.; Lim, B.; Yew, W.S.
    Glycine decarboxylase is an unusual amino acid decarboxylase involved in tumorigenesis (2014), Biochemistry, 53, 947-956 .
    View publication on PubMed
Search for more literature for 1.4.4.2

Activating Compound

Activating Compound Comment Organism Structure
H-protein upon addition of exogenous unlipoylated H-protein, kcat increases 190fold, in the absence of the lipoic acid moiety on H-protein, the methylamine adduct with pyridoxal 5'-phosphate (aminomethyl-quinonoid intermediate) is released as the product of the GLDC-catalyzed decarboxylation of glycine Homo sapiens
lipoylated H-protein the presence of the lipoyl moiety on H-protein does not affect the rates of GLDC (or GLDCcoexp)-catalyzed glycine decarboxylation Homo sapiens
additional information the presence of the lipoyl moiety on H-protein does not affect the rates of GLDC (or GLDCcoexp)-catalyzed glycine decarboxylation further corroborates the suggestion that H-protein (or lipoylated H-protein) does not directly participate in and is not required for release of CO2 from glycine in the formation of the pyridoxal 5'-phosphate-quinonoid intermediate, an important distinction that is contrary to earlier findings Homo sapiens

Cloned(Commentary)

Cloned (Comment) Organism
recombinant expression of codon optimized C-terminally His6-tagged enzyme GLDC in Escherichia coli strain BL21(DE3), GLDC is expressed either separately (without H-protein) or simultaneously with H-protein, coexpression of His6-tagged enzyme with codon-optimized human H-protein in Escherichia coli strain BL21(DE3) from pJexpress-416 vector Homo sapiens

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.0003
-
 glycine pH 7.0, 25°C, recombinant coexpressed wild-type enzyme Homo sapiens
0.00031
-
 glycine pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of lipoylated H-protein Homo sapiens
0.00037
-
 glycine pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of H-protein Homo sapiens
1.3
-
 glycine pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of lipoylated H-protein Homo sapiens
2.1
-
 glycine pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of H-protein Homo sapiens

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Homo sapiens

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
glycine + [glycine-cleavage complex H protein]-N6-lipoyl-L-lysine Homo sapiens
-
 [glycine-cleavage complex H protein]-S-aminomethyl-N6-dihydrolipoyl-L-lysine + CO2
-
 r

Organism

Organism UniProt Comment Textmining
Homo sapiens P23378
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant His6-tagged enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and dialysis Homo sapiens

Reaction

Reaction Comment Organism Reaction ID
glycine + [glycine-cleavage complex H protein]-N6-lipoyl-L-lysine = [glycine-cleavage complex H protein]-S-aminomethyl-N6-dihydrolipoyl-L-lysine + CO2 mechanism of the GLDC-catalyzed reaction, detailed overview. GLDC is an unusual PLP-containing alpha-amino acid decarboxylase that removes carbon dioxide from the glycine substrate without releasing the expected amine (methylamine, a metabolic precursor of toxic formaldehyde) as a product. In an unusual decarboxylation mechanism, the resulting aminomethyl moiety is instead transferred to an accessory H-protein. (1) H-Protein is not required for glycine decarboxylation but, instead, is required for the release of the aminomethyl moiety from the quinonoid adduct. (2) Glycine decarboxylation is reversible and presumably proceeds through a stable quinonoid intermediate. (3) The physiological product of glycine decarboxylation is H-protein-S-aminomethyl dihydrolipoyllysine and not methylamine (in the absence of H-protein, the aminomethyl moiety remains as a quinonoid adduct) Homo sapiens
a

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
glycine + [glycine-cleavage complex H protein]-N6-lipoyl-L-lysine
-
 Homo sapiens [glycine-cleavage complex H protein]-S-aminomethyl-N6-dihydrolipoyl-L-lysine + CO2
-
 r
glycine + [glycine-cleavage complex H protein]-N6-lipoyl-L-lysine reversible reaction Homo sapiens [glycine-cleavage complex H protein]-S-aminomethyl-N6-dihydrolipoyl-L-lysine + CO2
-
 r
additional information presence of excess pyridoxal 5'-phosphate is used in the assay mixture to facilitate the displacement of the quinonoid intermediate in the absence of an acceptor for the methylamine moiety (of decarboxylated glycine) to allow multiple enzyme turnovers. Mass spectrometry and 13C NMR spectroscopy are used to determine the products of glycine decarboxylation. The assay reaction mixtures are incubated for 1 week at pH 7.0, 25°C Homo sapiens ?
-
 ?

Subunits

Subunits Comment Organism
monomer 1 * 112730, mass spectrometry Homo sapiens
More recombinant human GLDC is active in the monomeric form, unlike GLDC orthologues in chicken and Synechocystis where the enzyme exists as a homodimer Homo sapiens

Synonyms

Synonyms Comment Organism
GLDC
-
 Homo sapiens
glycine decarboxylase
-
 Homo sapiens

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
25
-
 assay at Homo sapiens

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
0.0001
-
 glycine pH 7.0, 25°C, recombinant individually expressed wild-type enzyme Homo sapiens
0.00014
-
 glycine pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of lipoic acid Homo sapiens
0.016
-
 glycine pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of lipoylated H-protein Homo sapiens
0.019
-
 glycine pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of H-protein Homo sapiens
0.031
-
 glycine pH 7.0, 25°C, recombinant coexpressed wild-type enzyme Homo sapiens
0.033
-
 glycine pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of H-protein Homo sapiens
0.047
-
 glycine pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of lipoylated H-protein Homo sapiens

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7
-
 assay at Homo sapiens

Cofactor

Cofactor Comment Organism Structure
pyridoxal 5'-phosphate
-
 Homo sapiens

General Information

General Information Comment Organism
physiological function glycine decarboxylase is an unusual amino acid decarboxylase involved in tumorigenesis. In humans, GLDC is part of a multienzyme complex (which includes the lipoyl-containing H-protein) that couples the decarboxylation of glycine to the biosynthesis of serine Homo sapiens

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.009
-
 glycine pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of H-protein Homo sapiens
0.012
-
 glycine pH 7.0, 25°C, recombinant individually expressed wild-type enzyme in presence of lipoylated H-protein Homo sapiens
100
-
 glycine pH 7.0, 25°C, recombinant coexpressed wild-type enzyme Homo sapiens
150
-
 glycine pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of lipoylated H-protein Homo sapiens
890
-
 glycine pH 7.0, 25°C, recombinant coexpressed wild-type enzyme in presence of H-protein Homo sapiens