1WYT | pdb_00001wyt

Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in apo form

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1wytd_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Glycine dehydrogenase subunits (GDC-P)	Glycine dehydrogenase subunit 2 (P-protein)	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d1wytb1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Glycine dehydrogenase subunits (GDC-P)	Glycine dehydrogenase subunit 2 (P-protein)	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
C	d1wytc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Glycine dehydrogenase subunits (GDC-P)	Glycine dehydrogenase (decarboxylating) subunit 1	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
A	d1wyta1	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Glycine dehydrogenase subunits (GDC-P)	Glycine dehydrogenase (decarboxylating) subunit 1	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	PLP-dependent transferases	8033407	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8033407	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8033406	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8033406	3000954	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Med26	e1wytD1	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: Med26	ECOD (v294.1)
B	Med26	e1wytB1	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: Med26	ECOD (v294.1)
C	Med26	e1wytC1	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: Med26	ECOD (v294.1)
A	Med26	e1wytA1	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: Med26	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	6.20.440.10	Special	Other non-globular	Translocated Intimin Receptor	Chain T	CATH (4.3.0)
D	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B	6.20.440.10	Special	Other non-globular	Translocated Intimin Receptor	Chain T	CATH (4.3.0)
B	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
C	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, 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, C	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
B, D	glycine dehydrogenase subunit 2 (P-protein)	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 cation binding organic acid binding binding ion binding anion binding glycine binding amino acid binding carboxylic acid 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 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	glycine decarboxylation via glycine cleavage system 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 glycine decarboxylation via glycine cleavage system 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	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex oxidoreductase complex transferase complex glycine cleavage complex
A, C	glycine dehydrogenase (decarboxylating) subunit 1	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	nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process carbohydrate derivative metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process nucleoside metabolic process glycine decarboxylation via glycine cleavage system catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process organic acid catabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process carbohydrate derivative metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process nucleoside metabolic process glycine decarboxylation via glycine cleavage system catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid 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 small molecule catabolic process amino acid catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR049316	Glycine dehydrogenase, C-terminal domain	Domain
B, D	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
B, D	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
B, D	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
B, D	IPR020581	Glycine cleavage system P protein	Family
B, D	IPR023012	Probable glycine dehydrogenase (decarboxylating) subunit 2	Family
A, C	IPR023010	Probable glycine dehydrogenase (decarboxylating) subunit 1	Family
A, C	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, C	IPR049315	Glycine cleavage system P-protein, N-terminal domain	Domain
A, C	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, C	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, C	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.