EzCatDB: M00163
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DB codeM00163
CATH domainDomain 1-.-.-.-
Domain 2-.-.-.-
Domain 33.-.-.-
Domain 42.-.-.-
Domain 52.40.50.100 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Domain 63.50.50.60 : FAD/NAD(P)-binding domainCatalytic domain
Domain 73.50.50.60 : FAD/NAD(P)-binding domain
Domain 83.30.390.30 : Enolase-like; domain 1Catalytic domain
E.C.1.4.4.2,2.1.2.10,1.8.1.4

CATH domainRelated DB codes (homologues)
2.40.50.100 : OB fold (Dihydrolipoamide Acetyltransferase, E2P)M00222,M00145,M00188,M00189,T00223,M00190,M00191,M00208
3.30.390.30 : Enolase-like; domain 1T00017,T00213,T00233,T00242
3.50.50.60 : FAD/NAD(P)-binding domainD00015,D00041,D00042,D00045,D00064,D00071,T00004,T00015,T00017,T00025,T00211,T00213,T00233,T00242

Enzyme Name
UniProtKBKEGG

P49095P26969P23378P48015P49364P48728P39726P16048P23434P09624P31023P09622
Protein nameGlycine dehydrogenase [decarboxylating], mitochondrialGlycine dehydrogenase [decarboxylating], mitochondrialGlycine dehydrogenase [decarboxylating], mitochondrialAminomethyltransferase, mitochondrialAminomethyltransferase, mitochondrialAminomethyltransferase, mitochondrialGlycine cleavage system H protein, mitochondrialGlycine cleavage system H protein, mitochondrialGlycine cleavage system H protein, mitochondrialDihydrolipoyl dehydrogenase, mitochondrialDihydrolipoyl dehydrogenase, mitochondrialDihydrolipoyl dehydrogenase, mitochondrialglycine dehydrogenase (decarboxylating)
   (EC 1.4.4.2)

P-protein
   (EC 1.4.4.2)

glycine decarboxylase
   (EC 1.4.4.2)

glycine-cleavage complex
   (EC 1.4.4.2)

glycine:lipoylprotein oxidoreductase (decarboxylating andacceptor-aminomethylating)
   (EC 1.4.4.2)

protein P1
   (EC 1.4.4.2)

aminomethyltransferase
   (EC 2.1.2.10)

S-aminomethyldihydrolipoylprotein:(6S)-tetrahydrofolateaminomethyltransferase (ammonia-forming)
   (EC 2.1.2.10)

T-protein
   (EC 2.1.2.10)

glycine synthase
   (EC 2.1.2.10)

tetrahydrofolate aminomethyltransferase
   (EC 2.1.2.10)

[protein]-8-S-aminomethyldihydrolipoyllysine:tetrahydrofolateaminomethyltransferase (ammonia-forming)
   (EC 2.1.2.10)

dihydrolipoyl dehydrogenase
   (EC 1.8.1.4)

LDP-Glc
   (EC 1.8.1.4)

LDP-Val
   (EC 1.8.1.4)

dehydrolipoate dehydrogenase
   (EC 1.8.1.4)

diaphorase
   (EC 1.8.1.4)

dihydrolipoamide dehydrogenase
   (EC 1.8.1.4)

dihydrolipoamide:NAD+ oxidoreductase
   (EC 1.8.1.4)

dihydrolipoic dehydrogenase
   (EC 1.8.1.4)

dihydrothioctic dehydrogenase
   (EC 1.8.1.4)

lipoamide dehydrogenase (NADH)
   (EC 1.8.1.4)

lipoamide oxidoreductase (NADH)
   (EC 1.8.1.4)

lipoamide reductase
   (EC 1.8.1.4)

lipoamide reductase (NADH)
   (EC 1.8.1.4)

lipoate dehydrogenase
   (EC 1.8.1.4)

lipoic acid dehydrogenase
   (EC 1.8.1.4)

lipoyl dehydrogenase
   (EC 1.8.1.4)

protein-6-N-(dihydrolipoyl)lysine:NAD+ oxidoreductase
   (EC 1.8.1.4)

SynonymsEC 1.4.4.2
Glycine decarboxylase
Glycine decarboxylase complex subunit P
Glycine cleavage system P-protein
EC 1.4.4.2
Glycine decarboxylase
Glycine cleavage system P-protein
EC 1.4.4.2
Glycine decarboxylase
Glycine cleavage system P-protein
EC 2.1.2.10
Glycine decarboxylase complex subunit T
Glycine cleavage system T protein
GCVT
EC 2.1.2.10
Glycine cleavage system T protein
GCVT
EC 2.1.2.10
Glycine cleavage system T protein
GCVT
Glycine decarboxylase complex subunit H
NoneNoneEC 1.8.1.4
Dihydrolipoamide dehydrogenase
Lipoamide dehydrogenase component of pyruvate dehydrogenase complex
Pyruvate dehydrogenase complex E3 component
Glycine decarboxylase complex subunit L
EC 1.8.1.4
Dihydrolipoamide dehydrogenase
Pyruvate dehydrogenase complex E3 subunit
PDC-E3
E3
Glycine cleavage system L protein
EC 1.8.1.4
Dihydrolipoamide dehydrogenase
Glycine cleavage system L protein
RefSeqNP_013914.1 (Protein)
NM_001182695.1 (DNA/RNA sequence)

NP_000161.2 (Protein)
NM_000170.2 (DNA/RNA sequence)
NP_010302.1 (Protein)
NM_001180327.1 (DNA/RNA sequence)

NP_000472.2 (Protein)
NM_000481.3 (DNA/RNA sequence)
NP_001158182.1 (Protein)
NM_001164710.1 (DNA/RNA sequence)
NP_001158183.1 (Protein)
NM_001164711.1 (DNA/RNA sequence)
NP_001158184.1 (Protein)
NM_001164712.1 (DNA/RNA sequence)
NP_009355.3 (Protein)
NM_001178189.1 (DNA/RNA sequence)

NP_004474.2 (Protein)
NM_004483.4 (DNA/RNA sequence)
NP_116635.1 (Protein)
NM_001179948.1 (DNA/RNA sequence)

NP_000099.2 (Protein)
NM_000108.3 (DNA/RNA sequence)
PfamPF02347 (GDC-P)
[Graphical view]
PF02347 (GDC-P)
[Graphical view]
PF01212 (Beta_elim_lyase)
PF02347 (GDC-P)
[Graphical view]
PF01571 (GCV_T)
PF08669 (GCV_T_C)
[Graphical view]
PF01571 (GCV_T)
PF08669 (GCV_T_C)
[Graphical view]
PF01571 (GCV_T)
PF08669 (GCV_T_C)
[Graphical view]
PF01597 (GCV_H)
[Graphical view]
PF01597 (GCV_H)
[Graphical view]
PF01597 (GCV_H)
[Graphical view]
PF00070 (Pyr_redox)
PF07992 (Pyr_redox_2)
PF02852 (Pyr_redox_dim)
[Graphical view]
PF00070 (Pyr_redox)
PF07992 (Pyr_redox_2)
PF02852 (Pyr_redox_dim)
[Graphical view]
PF00070 (Pyr_redox)
PF07992 (Pyr_redox_2)
PF02852 (Pyr_redox_dim)
[Graphical view]

KEGG pathways
MAP codePathwaysE.C.
MAP00010Glycolysis / Gluconeogenesis1.8.1.4
MAP00020Citrate cycle (TCA cycle)1.8.1.4
MAP00260Glycine, serine and threonine metabolism1.4.4.2,2.1.2.10,1.8.1.4
MAP00280Valine, leucine and isoleucine degradation1.8.1.4
MAP00620Pyruvate metabolism1.8.1.4
MAP00670One carbon pool by folate2.1.2.10
MAP00910Nitrogen metabolism2.1.2.10

UniProtKB:Accession NumberP49095P26969P23378P48015P49364P48728P39726P16048P23434P09624P31023P09622
Entry nameGCSP_YEASTGCSP_PEAGCSP_HUMANGCST_YEASTGCST_PEAGCST_HUMANGCSH_YEASTGCSH_PEAGCSH_HUMANDLDH_YEASTDLDH_PEADLDH_HUMAN
ActivityGlycine + H-protein-lipoyllysine = H-protein- S-aminomethyldihydrolipoyllysine + CO(2).Glycine + H-protein-lipoyllysine = H-protein- S-aminomethyldihydrolipoyllysine + CO(2).Glycine + H-protein-lipoyllysine = H-protein- S-aminomethyldihydrolipoyllysine + CO(2).[Protein]-S(8)-aminomethyldihydrolipoyllysine + tetrahydrofolate = [protein]-dihydrolipoyllysine + 5,10- methylenetetrahydrofolate + NH(3).[Protein]-S(8)-aminomethyldihydrolipoyllysine + tetrahydrofolate = [protein]-dihydrolipoyllysine + 5,10- methylenetetrahydrofolate + NH(3).[Protein]-S(8)-aminomethyldihydrolipoyllysine + tetrahydrofolate = [protein]-dihydrolipoyllysine + 5,10- methylenetetrahydrofolate + NH(3).


Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH.Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH.Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH.
SubunitComponent of the glycine decarboxylase complex (GDC), which is composed of four proteins: P, T, L and H.Homodimer. The glycine cleavage system is composed of four proteins: P, T, L and H.Homodimer. The glycine cleavage system is composed of four proteins: P, T, L and H.Component of the glycine decarboxylase complex (GDC), which is composed of four proteins: P, T, L and H.The glycine cleavage system is composed of four proteins: P, T, L and H.The glycine cleavage system is composed of four proteins: P, T, L and H.Component of the glycine decarboxylase complex (GDC), which is composed of four proteins: P, T, L and H.The glycine cleavage system is composed of four proteins: P, T, L and H.The glycine cleavage system is composed of four proteins: P, T, L and H.LPD1 is a homodimer. Eukaryotic pyruvate dehydrogenase (PDH) complexes are organized as a core consisting of the oligomeric dihydrolipoamide acetyl-transferase (E2), around which are arranged multiple copies of pyruvate dehydrogenase (E1), dihydrolipoamide dehydrogenase (E3) and protein X (E3BP) bound by non-covalent bonds. LPD1 is a component of the glycine decarboxylase complex (GDC), which is composed of four proteins: P, T, L and H.Homodimer.Homodimer. Eukaryotic pyruvate dehydrogenase complexes are organized about a core consisting of the oligomeric dihydrolipoamide acetyl-transferase, around which are arranged multiple copies of pyruvate dehydrogenase, dihydrolipoamide dehydrogenase and protein X bound by non-covalent bonds.
Subcellular locationMitochondrion (By similarity).Mitochondrion.Mitochondrion.Mitochondrion.Mitochondrion.Mitochondrion.Mitochondrion.Mitochondrion.Mitochondrion.Mitochondrion matrix.Mitochondrion matrix.Mitochondrion matrix.
CofactorPyridoxal phosphate (By similarity).Pyridoxal phosphate.Pyridoxal phosphate.


Binds 1 lipoyl cofactor covalently (By similarity).Binds 1 lipoyl cofactor covalently.Binds 1 lipoyl cofactor covalently.Binds 1 FAD per subunit (By similarity).Binds 1 FAD per subunit.Binds 1 FAD per subunit (By similarity).

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00018C00016C00037C02051C01242C00101C02972C00003C01242C00011C02972C00143C00014C02051C00004C00080
E.C.1.4.4.21.8.1.41.4.4.21.4.4.22.1.2.102.1.2.101.8.1.41.8.1.41.4.4.21.4.4.22.1.2.102.1.2.102.1.2.101.8.1.41.8.1.41.8.1.4
CompoundPyridoxal phosphateFADGlycineLipoylproteinS-AminomethyldihydrolipoylproteinTetrahydrofolateDihydrolipoylproteinNAD+S-AminomethyldihydrolipoylproteinCO2Dihydrolipoylprotein5,10-methylenetetrahydrofolateNH3LipoylproteinNADHH+
Typearomatic ring (with nitrogen atoms),phosphate group/phosphate ionamide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,nucleotideamino acidsdisulfide bond,lipid,peptide/proteinamine group,lipid,peptide/protein,sulfhydryl group,sulfide groupamino acids,amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carboxyl groupcarbohydrate,lipid,peptide/protein,sulfhydryl groupamide group,amine group,nucleotideamine group,lipid,peptide/protein,sulfhydryl group,sulfide groupotherscarbohydrate,lipid,peptide/protein,sulfhydryl groupamino acids,amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carboxyl groupamine group,organic iondisulfide bond,lipid,peptide/proteinamide group,amine group,nucleotideothers
ChEBI18405
16238
15428
57305


15635
20506

15846

16526


16134

16908
15378
PubChem1051
643975
750
5257127


91443
5460413

5893

280

439175
222

439153
1038
                        
1wsrA01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1wsrB01UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1wsvA01UnboundUnboundUnboundUnboundUnboundAnalogue:THHUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1wsvB01UnboundUnboundUnboundUnboundUnboundAnalogue:THHUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1wsrA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1wsrB02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1wsvA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1wsvB02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1dxmAUnboundUnboundUnboundUnboundUnboundUnboundBound:REDUnboundUnboundUnboundBound:REDUnboundUnboundUnboundUnbound 
1dxmBUnboundUnboundUnboundUnboundUnboundUnboundBound:REDUnboundUnboundUnboundBound:REDUnboundUnboundUnboundUnbound 
1hpcAUnboundUnboundUnboundBound:LPAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundBound:LPAUnbound 
1hpcBUnboundUnboundUnboundBound:LPAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundBound:LPAUnbound 
1htpAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1jehA01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1jehB01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1v59A01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1v59B01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1dxlA01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1dxlB01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1dxlC01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1dxlD01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcA01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcB01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcC01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcD01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcE01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcF01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcG01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcH01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdA01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdB01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdC01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdD01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdE01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdF01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdG01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdH01UnboundBound:FADUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1jehA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1jehB02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1v59A02UnboundUnboundUnboundUnboundUnboundUnboundUnboundAnalogue:NADUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1v59B02UnboundUnboundUnboundUnboundUnboundUnboundUnboundAnalogue:NADUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1dxlA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1dxlB02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1dxlC02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1dxlD02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundBound:NADUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcB02UnboundUnboundUnboundUnboundUnboundUnboundUnboundAnalogue:NADUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcC02UnboundUnboundUnboundUnboundUnboundUnboundUnboundAnalogue:NADUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcD02UnboundUnboundUnboundUnboundUnboundUnboundUnboundBound:NADUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcE02UnboundUnboundUnboundUnboundUnboundUnboundUnboundAnalogue:NADUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcF02UnboundUnboundUnboundUnboundUnboundUnboundUnboundAnalogue:NADUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcG02UnboundUnboundUnboundUnboundUnboundUnboundUnboundAnalogue:NADUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcH02UnboundUnboundUnboundUnboundUnboundUnboundUnboundAnalogue:NADUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdA02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundBound:NAI 
1zmdB02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundBound:NAI 
1zmdC02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundBound:NAI 
1zmdD02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundBound:NAI 
1zmdE02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundBound:NAI 
1zmdF02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundBound:NAI 
1zmdG02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundBound:NAI 
1zmdH02UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundBound:NAI 
1jehA03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1jehB03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1v59A03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1v59B03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1dxlA03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1dxlB03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1dxlC03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1dxlD03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcA03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcB03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcC03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcD03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcE03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcF03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcG03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmcH03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdA03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdB03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdC03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdD03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdE03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdF03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdG03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 
1zmdH03UnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound 

Active-site residues
resource
literature [20] & see T00017
pdbCatalytic residuesCofactor-binding residues
          
1wsrA01ASP 101
 
1wsrB01ASP 101
 
1wsvA01ASP 101
 
1wsvB01ASP 101
 
1wsrA02 
 
1wsrB02 
 
1wsvA02 
 
1wsvB02 
 
1dxmA 
LYS 63(lipoyl cofactor binding)
1dxmB 
LYS 63(lipoyl cofactor binding)
1hpcA 
LYS 63(lipoyl cofactor binding)
1hpcB 
LYS 63(lipoyl cofactor binding)
1htpA 
LYS 63(lipoyl cofactor binding)
1jehA01TYR 18;CYS 44;CYS 49
 
1jehB01TYR 18;CYS 44;CYS 49
 
1v59A01TYR 18;CYS 44;CYS 49
 
1v59B01TYR 18;CYS 44;CYS 49
 
1dxlA01TYR 19;CYS 45;CYS 50
 
1dxlB01TYR 19;CYS 45;CYS 50
 
1dxlC01TYR 19;CYS 45;CYS 50
 
1dxlD01TYR 19;CYS 45;CYS 50
 
1zmcA01TYR 19;CYS 45;CYS 50
 
1zmcB01TYR 19;CYS 45;CYS 50
 
1zmcC01TYR 19;CYS 45;CYS 50
 
1zmcD01TYR 19;CYS 45;CYS 50
 
1zmcE01TYR 19;CYS 45;CYS 50
 
1zmcF01TYR 19;CYS 45;CYS 50
 
1zmcG01TYR 19;CYS 45;CYS 50
 
1zmcH01TYR 19;CYS 45;CYS 50
 
1zmdA01TYR 19;CYS 45;CYS 50
 
1zmdB01TYR 19;CYS 45;CYS 50
 
1zmdC01TYR 19;CYS 45;CYS 50
 
1zmdD01TYR 19;CYS 45;CYS 50
 
1zmdE01TYR 19;CYS 45;CYS 50
 
1zmdF01TYR 19;CYS 45;CYS 50
 
1zmdG01TYR 19;CYS 45;CYS 50
 
1zmdH01TYR 19;CYS 45;CYS 50
 
1jehA02 
 
1jehB02 
 
1v59A02 
 
1v59B02 
 
1dxlA02 
 
1dxlB02 
 
1dxlC02 
 
1dxlD02 
 
1zmcA02 
 
1zmcB02 
 
1zmcC02 
 
1zmcD02 
 
1zmcE02 
 
1zmcF02 
 
1zmcG02 
 
1zmcH02 
 
1zmdA02 
 
1zmdB02 
 
1zmdC02 
 
1zmdD02 
 
1zmdE02 
 
1zmdF02 
 
1zmdG02 
 
1zmdH02 
 
1jehA03HIS 457;HIS 477
 
1jehB03HIS 457;HIS 477
 
1v59A03HIS 457;HIS 477
 
1v59B03HIS 457;HIS 477
 
1dxlA03HIS 449;HIS 469
 
1dxlB03HIS 449;HIS 469
 
1dxlC03HIS 449;HIS 469
 
1dxlD03HIS 449;HIS 469
 
1zmcA03HIS 452;ASN 473
 
1zmcB03HIS 452;ASN 473
 
1zmcC03HIS 452;ASN 473
 
1zmcD03HIS 452;ASN 473
 
1zmcE03HIS 452;ASN 473
 
1zmcF03HIS 452;ASN 473
 
1zmcG03HIS 452;ASN 473
 
1zmcH03HIS 452;ASN 473
 
1zmdA03HIS 452;ASN 473
 
1zmdB03HIS 452;ASN 473
 
1zmdC03HIS 452;ASN 473
 
1zmdD03HIS 452;ASN 473
 
1zmdE03HIS 452;ASN 473
 
1zmdF03HIS 452;ASN 473
 
1zmdG03HIS 452;ASN 473
 
1zmdH03HIS 452;ASN 473
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[20]Fig.3, p.1148-1151

references
[1]
PubMed ID6750353
JournalMol Cell Biochem
Year1982
Volume45
Pages137-49
AuthorsKikuchi G, Hiraga K
TitleThe mitochondrial glycine cleavage system. Unique features of the glycine decarboxylation.
[2]
PubMed ID1856858
JournalJ Mol Biol
Year1991
Volume220
Pages223-4
AuthorsSieker L, Cohen-Addad C, Neuburger M, Douce R
TitleCrystallographic data for H-protein from the glycine decarboxylase complex.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS)
Medline ID94255425
PubMed ID8197146
JournalProc Natl Acad Sci U S A
Year1994
Volume91
Pages4850-3
AuthorsPares S, Cohen-Addad C, Sieker L, Neuburger M, Douce R
TitleX-ray structure determination at 2.6-A resolution of a lipoate-containing protein: the H-protein of the glycine decarboxylase complex from pea leaves.
Related UniProtKBP16048
[4]
CommentsX-ray crystallography
JournalActa Crystallogr D Biol Crystallogr
Year1995
Volume51
Pages1041-51
AuthorsPares S, Cohenaddad C, Sieker LC, Neuburger M, Douce R
TitleRefined structures at 2 and 2.2 A resolution of two forms of the H-protein, a lipoamide-containing protein of the glycine decarboxylase complex.
Related PDB1hpc
[5]
CommentsX-ray crystallography
PubMed ID7719855
JournalNat Struct Biol
Year1995
Volume2
Pages63-8
AuthorsCohen-Addad C, Pares S, Sieker L, Neuburger M, Douce R
TitleThe lipoamide arm in the glycine decarboxylase complex is not freely swinging.
Related PDB1htp
[6]
PubMed ID8830251
JournalMol Microbiol
Year1996
Volume19
Pages611-23
AuthorsSinclair DA, Hong SP, Dawes IW
TitleSpecific induction by glycine of the gene for the P-subunit of glycine decarboxylase from Saccharomyces cerevisiae.
[7]
PubMed ID9479445
JournalBiochimie
Year1997
Volume79
Pages637-43
AuthorsCohen-Addad C, Faure M, Neuburger M, Ober R, Sieker L, Bourguignon J, Macherel D, Douce R
TitleStructural studies of the glycine decarboxylase complex from pea leaf mitochondria.
[8]
PubMed ID9538259
JournalJ Biochem (Tokyo)
Year1998
Volume123
Pages668-74
AuthorsToyoda T, Suzuki K, Sekiguchi T, Reed LJ, Takenaka A
TitleCrystal structure of eucaryotic E3, lipoamide dehydrogenase from yeast.
Related PDB1jeh
[9]
PubMed ID10387079
JournalBiochemistry
Year1999
Volume38
Pages8334-46
AuthorsGuilhaudis L, Simorre JP, Blackledge M, Neuburger M, Bourguignon J, Douce R, Marion D, Gans P
TitleInvestigation of the local structure and dynamics of the H subunit of the mitochondrial glycine decarboxylase using heteronuclear NMR spectroscopy.
[10]
PubMed ID10375564
JournalCurr Opin Plant Biol
Year1999
Volume2
Pages214-22
AuthorsDouce R, Neuburger M
TitleBiochemical dissection of photorespiration.
[11]
PubMed ID10473591
JournalJ Biol Chem
Year1999
Volume274
Pages26344-52
AuthorsGueguen V, Macherel D, Neuburger M, Pierre CS, Jaquinod M, Gans P, Douce R, Bourguignon J
TitleStructural and functional characterization of H protein mutants of the glycine decarboxylase complex.
[12]
PubMed ID10605092
JournalJ Biomol NMR
Year1999
Volume15
Pages185-6
AuthorsGuilhaudis L, Simorre JP, Bouchayer E, Neuburger M, Bourguignon J, Douce R, Marion D, Gans P
TitleBackbone and sequence-specific assignment of three forms of the lipoate-containing H-protein of the glycine decarboxylase complex.
[13]
PubMed ID10398369
JournalProteins
Year1999
Volume36
Pages228-37
AuthorsRoche O, Hinsen K, Field MJ
TitleTheoretical study of the conformation of the H-protein lipoamide arm as a function of its terminal group.
[14]
PubMed ID10757974
JournalBiochemistry
Year2000
Volume39
Pages4259-66
AuthorsGuilhaudis L, Simorre JP, Blackledge M, Marion D, Gans P, Neuburger M, Douce R
TitleCombined structural and biochemical analysis of the H-T complex in the glycine decarboxylase cycle: evidence for a destabilization mechanism of the H-protein.
[15]
CommentsX-ray crystallography
PubMed ID10806386
JournalEur J Biochem
Year2000
Volume267
Pages2890-8
AuthorsFaure M, Bourguignon J, Neuburger M, MacHerel D, Sieker L, Ober R, Kahn R, Cohen-Addad C, Douce R
TitleInteraction between the lipoamide-containing H-protein and the lipoamide dehydrogenase (L-protein) of the glycine decarboxylase multienzyme system 2. Crystal structures of H- and L-proteins.
Related PDB1dxm,1dxl
[16]
PubMed ID10806385
JournalEur J Biochem
Year2000
Volume267
Pages2882-9
AuthorsNeuburger M, Polidori AM, Pietre E, Faure M, Jourdain A, Bourguignon J, Pucci B, Douce R
TitleInteraction between the lipoamide-containing H-protein and the lipoamide dehydrogenase (L-protein) of the glycine decarboxylase multienzyme system. 1. Biochemical studies.
[17]
PubMed ID11599027
JournalProteins
Year2001
Volume45
Pages237-40
AuthorsRoche O, Field MJ
TitleTheoretical study of the conformation of the lipoamide arm in a mutant H protein.
[18]
PubMed ID11286922
JournalTrends Plant Sci
Year2001
Volume6
Pages167-76
AuthorsDouce R, Bourguignon J, Neuburger M, Rebeille F
TitleThe glycine decarboxylase system: a fascinating complex.
[19]
PubMed ID15946682
JournalJ Mol Biol
Year2005
Volume350
Pages543-52
AuthorsBrautigam CA, Chuang JL, Tomchick DR, Machius M, Chuang DT
TitleCrystal structure of human dihydrolipoamide dehydrogenase: NAD+/NADH binding and the structural basis of disease-causing mutations.
Related PDB1zmc,1zmd
[20]
PubMed ID16051266
JournalJ Mol Biol
Year2005
Volume351
Pages1146-59
AuthorsOkamura-Ikeda K, Hosaka H, Yoshimura M, Yamashita E, Toma S, Nakagawa A, Fujiwara K, Motokawa Y, Taniguchi H
TitleCrystal structure of human T-protein of glycine cleavage system at 2.0 A resolution and its implication for understanding non-ketotic hyperglycinemia.
Related PDB1wsr,1wsv

comments
The glycine cleavage system, which catalyzes three distinct reactions (EC 1.4.4.2, 2.1.2.10, 1.8.1.4) is a protein comprex composed of the four proteins:
P chain is responsible for the cleavage of glycine (EC 1.4.4.2).
T chain is responsible for the transfer of aminomethyl group (EC 2.1.2.10).
H chain transports methylamine group from the P chain to the T chain, with the lysine residue (Lys63) covalently-bound to lipoyl group.
L chain is responsible for the oxidation of dihydrolipoyl group (EC 1.8.1.4). This enzyme is homologous to the counterpart enzyme (T00017 in EzCatDB).
Although the structures of T, H and L chain have been determined, those of the other chain have not been solved yet.
As for the reaction by T chain (EC 2.1.2.10), the two consecutive transfer reactions might be involved (see [20]).

createdupdated
2004-01-292009-03-13


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
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