Annotations: 6I35

Crystal structure of human glycine decarboxylase (P-protein) bound with pyridoxyl-glycine-5'-monophosphate

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	ATP-synt	e6i35D2	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: ATP-synt	ECOD (v295.2)
D	Cation_ATPase_C,Cation_ATPase_N	e6i35D1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Class I glutamine amidotransferase-like	F: Cation_ATPase_C,Cation_ATPase_N	ECOD (v295.2)
C	ATP-synt	e6i35C1	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: ATP-synt	ECOD (v295.2)
B	ATP-synt	e6i35B1	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: ATP-synt	ECOD (v295.2)
B	Cation_ATPase_C,Cation_ATPase_N	e6i35B2	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Class I glutamine amidotransferase-like	F: Cation_ATPase_C,Cation_ATPase_N	ECOD (v295.2)
A	ATP-synt	e6i35A1	A: alpha arrays	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat)	T: Acyl-CoA N-acyltransferases (Nat)	F: ATP-synt	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01212	Beta-eliminating lyase (Beta_elim_lyase)	Beta-eliminating lyase		Domain
A, B, C, D	PF21478	Glycine dehydrogenase, C-terminal domain (GcvP2_C)	Glycine dehydrogenase, C-terminal domain	This entry includes Glycine dehydrogenases, also known as glycine cleavage system P protein, which bind the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO2 is released and the remaining methylamine moiety is then transferre ...	This entry includes Glycine dehydrogenases, also known as glycine cleavage system P protein, which bind the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO2 is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. The monomer consists of two domains, a large domain and a small domain. This entry represents the small domain, which has a complex alpha/beta structure [1,2].	Domain
A, B, C, D	PF02347	Glycine cleavage system P-protein (GDC-P)	Glycine cleavage system P-protein	This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1.2.10 (GDC) also annotated as glycine cleavage system or ...	This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1.2.10 (GDC) also annotated as glycine cleavage system or glycine synthase. GDC consists of four proteins P, H, L and T [2]. The reaction catalysed by this protein is:- Glycine + lipoylprotein <=> S-aminomethyldihydrolipoylprotein + CO2	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Glycine dehydrogenase (decarboxylating), mitochondrial	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity oxidoreductase activity, acting on the CH-NH2 group of donors glycine dehydrogenase (decarboxylating) activity oxidoreductase activity catalytic activity oxidoreductase activity, acting on the CH-NH2 group of donors, disulfide as acceptor lyase activity cation binding vitamin binding vitamin B6 binding identical protein binding protein binding binding protein homodimerization activity protein dimerization activity oxidoreductase activity, acting on the CH-NH2 group of donors glycine dehydrogenase (decarboxylating) activity oxidoreductase activity catalytic activity oxidoreductase activity, acting on the CH-NH2 group of donors, disulfide as acceptor lyase activity cation binding vitamin binding vitamin B6 binding pyridoxal binding ion binding heterocyclic compound binding small molecule binding electron transfer activity	response to amine response to stimulus response to chemical response to methylamine response to nitrogen compound response to lipoic acid response to lipid response to fatty acid response to oxygen-containing compound glycine decarboxylation via glycine cleavage system catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process response to amine response to stimulus response to chemical response to methylamine response to nitrogen compound response to lipoic acid response to lipid response to fatty acid response to oxygen-containing compound glycine decarboxylation via glycine cleavage system catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process glycine metabolic process proteinogenic amino acid metabolic process proteinogenic amino acid catabolic process glycine catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process small molecule catabolic process amino acid catabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex transferase complex glycine cleavage complex membrane-enclosed lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex transferase complex glycine cleavage complex membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR049316	Glycine dehydrogenase, C-terminal domain	Domain
A, B, C, D	IPR001597	Aromatic amino acid beta-eliminating lyase/threonine aldolase	Domain
A, B, C, D	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C, D	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B, C, D	IPR003437	Glycine dehydrogenase (decarboxylating)	Family
A, B, C, D	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D	IPR049315	Glycine cleavage system P-protein, N-terminal domain	Domain
A, B, C, D	IPR020581	Glycine cleavage system P protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	: P23378	glycine encephalopathy pituitary cancer breast cancer glioblastoma Hyperglycinemia, Nonketotic, Type II inborn errors of metabolism malignant glioma oligodendroglioma pancreatic ductal adenocarcinoma psoriasis intellectual disability malignant pancreatic neoplasm osteosarcoma pilocytic astrocytoma exocrine pancreatic carcinoma glycine encephalopathy pituitary cancer breast cancer glioblastoma Hyperglycinemia, Nonketotic, Type II inborn errors of metabolism malignant glioma oligodendroglioma pancreatic ductal adenocarcinoma psoriasis intellectual disability malignant pancreatic neoplasm osteosarcoma pilocytic astrocytoma exocrine pancreatic carcinoma lung cancer medulloblastoma ovarian cancer