6I34 | pdb_00006i34

Crystal structure of Neanderthal glycine decarboxylase (P-protein)

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	GcvP2	e6i34D2	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)
D	GDC-P_C	e6i34D1	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)
D	GDC-P_N	e6i34D3	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)
D	Aminotran_5_N	e6i34D4	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
C	GcvP2	e6i34C3	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)
C	GDC-P_C	e6i34C2	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)
C	GDC-P_N	e6i34C4	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)
C	Aminotran_5_N	e6i34C1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
B	GcvP2	e6i34B2	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	e6i34B1	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	GDC-P_N	e6i34B3	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)
B	Aminotran_5_N	e6i34B4	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
A	GcvP2	e6i34A2	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	e6i34A1	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	e6i34A4	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_5_N	e6i34A3	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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	PF01212	Beta-eliminating lyase (Beta_elim_lyase)	Beta-eliminating lyase		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	Neanderthal Glycine decarboxylase	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule 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 lyase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule 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 lyase activity electron transfer activity cation binding organic acid binding glycine binding amino acid binding carboxylic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity pyridoxal binding	response to lipoic acid response to lipid response to stimulus response to fatty acid response to chemical response to oxygen-containing compound catabolic 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 response to lipoic acid response to lipid response to stimulus response to fatty acid response to chemical response to oxygen-containing compound catabolic 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 alpha-amino acid catabolic 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 response to amine response to methylamine response to nitrogen compound glycine decarboxylation via glycine cleavage system response to peptide response to cytokine response to leukemia inhibitory factor cellular response to cytokine stimulus cellular response to leukemia inhibitory factor	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell periphery plasma membrane membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex catalytic complex oxidoreductase complex transferase complex glycine cleavage complex mitochondrial matrix

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR001597	Aromatic amino acid beta-eliminating lyase/threonine aldolase	Domain
A, B, C, D	IPR003437	Glycine dehydrogenase (decarboxylating)	Family
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
A, B, C, D	IPR049316	Glycine dehydrogenase, C-terminal domain	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	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: 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

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.