4LGL | pdb_00004lgl

Crystal Structure of Glycine Decarboxylase P-protein from Synechocystis sp. PCC 6803, apo form

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	GcvP2	e4lglA2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: GcvP2	ECOD (1.6)
A	GDC-P_C	e4lglA4	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: GDC-P_C	ECOD (1.6)
A	GDC-P_N	e4lglA1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: GDC-P_N	ECOD (1.6)
A	Aminotran_1_2_N	e4lglA5	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_1_2_N	ECOD (1.6)
B	GcvP2	e4lglB6	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: GcvP2	ECOD (1.6)
B	GDC-P_C	e4lglB4	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: GDC-P_C	ECOD (1.6)
B	Aminotran_1_2_N	e4lglB5	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_1_2_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	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	Glycine dehydrogenase [decarboxylating]	cation binding organic acid binding binding ion binding anion binding glycine binding amino acid binding carboxylic acid binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding heterocyclic compound binding oxidoreductase activity, acting on the CH-NH2 group of donors cation binding organic acid binding binding ion binding anion binding glycine binding amino acid binding carboxylic acid binding small molecule binding vitamin binding vitamin B6 binding pyridoxal phosphate binding heterocyclic compound binding 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	glycine decarboxylation via glycine cleavage system catabolic process serine family amino acid metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process glycine metabolic process proteinogenic amino acid metabolic process serine family amino acid catabolic process proteinogenic amino acid catabolic process alpha-amino acid catabolic process glycine decarboxylation via glycine cleavage system catabolic process serine family amino acid metabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process glycine metabolic process proteinogenic amino acid metabolic process serine family amino acid catabolic process proteinogenic amino acid catabolic process alpha-amino acid catabolic process glycine catabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process small molecule catabolic process amino acid catabolic process	protein-containing complex catalytic complex oxidoreductase complex glycine cleavage complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR049316	Glycine dehydrogenase, C-terminal domain	Domain
A, B	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B	IPR003437	Glycine dehydrogenase (decarboxylating)	Family
A, B	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B	IPR049315	Glycine cleavage system P-protein, N-terminal domain	Domain
A, B	IPR020581	Glycine cleavage system P protein	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.